Lymphocyte antigen cd5-like (cd5l)-interleukin 12b (p40)  heterodimers in immunity

ABSTRACT

Described herein are methods for suppressing an immune response in a subject, e.g., a subject with an autoimmune disease, by administering to the subject a therapeutically effective amount of recombinant CD5L, CD5L homodimers and/or CD5L:p40 heterodimers, or nucleic acids encoding any of these. Also described are methods for enhancing an immune response in a subject, e.g., a subject with cancer, infection, or an immune deficiency, by administering to the subject a therapeutically effective amount of an antibody or antigen-binding fragment thereof that binds specifically to CD5L, D5L homodimers and/or CD5L:p40 heterodimers, and inhibits their binding to the IL-23 receptor, or inhibits formation of the CD5L homodimer and/or CD5L:p40 heterodimer, or inhibitory nucleic acids that target CD5L and/or p40.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant Nos. P01AI056299, P01 AI039671, P01 AI073748, and 5P01 AI045757 awarded by theNational Institutes of Health. The Government has certain rights in theinvention.

TECHNICAL FIELD

Described herein are methods for suppressing or enhancing an immuneresponse in a subject.

BACKGROUND

The cytokine environment influences immune cell differentiation,function and plasticity. IL-23 has been identified as key player ininflammatory diseases, contributing largely to mucosal inflammation. Itwas discovered as a susceptibility gene in GWAS and is widely implicatedin autoimmune diseases and cancer such as melanoma and colorectalcarcinoma (Burkett et al., 2015; Cho and Feldman, 2015; Teng et al.,2015; Wang and Karin, 2015).

SUMMARY

The present invention is based, at least in part, on the discovery thatCD5L and p40 form heterodimers in vivo, and that these heterodimersmodulate the immune response. CD5L exists as a monomer, and is also ableto form dimers; both forms may also serve as immunomodulators. Someembodiments comprise methods for modulating an immune response orsuppressing an immune response (e.g., an inflammatory immune response)in a subject, the method comprising administering to the subject atherapeutically effective amount of recombinant soluble CD5L, aCD5L:CD5L homodimer, a CD5L:p40 heterodimer, or one or more nucleicacids encoding the same. In some embodiments, the subject has anautoimmune disease, e.g., Multiple Sclerosis (MS), Irritable BowelDisease (IBD), Crohn's disease, spondyloarthritides, Systemic LupusErythematosus (SLE), Vitiligo, rheumatoid arthritis, psoriasis,Sjögren's syndrome, or diabetes. In some embodiments, the subject has aninflammation-related cancer, e.g., colorectal cancer, carcinogen-inducedskin papilloma, fibrosarcoma, or mammary carcinomas.

Some embodiments comprise methods of suppressing an immune response in asubject, the method comprising administering to the subject atherapeutically effective amount of one or more of: a recombinantsoluble CD5L and/or a nucleic acid encoding CD5L; a recombinant solubleCD5L:CD5L homodimer and/or a nucleic acid encoding a CD5L homodimer; anda recombinant soluble CD5L:p40 heterodimer and/or nucleic acids encodingCD5L and p40. In some embodiments the subject has an autoimmune disease,such as Multiple Sclerosis (MS), Irritable Bowel Disease (IBD), Crohn'sdisease, spondyloarthritides, Systemic Lupus Erythematosus (SLE),Vitiligo, rheumatoid arthritis, psoriasis, Sjögren's syndrome, ordiabetes. In some embodiments, subject has an inflammation-relatedcancer, such as colorectal cancer, carcinogen-induced skin papilloma,fibrosarcoma, or mammary carcinomas.

Some embodiments comprise administering the CD4L:p40 heterodimer. Someembodiments comprise administering the CD5L:CD5L homodimer.

Some embodiments relate to methods of enhancing an immune response in asubject, the method comprising administering to the subject atherapeutically effective amount of an agent that: (a) inhibits CD5L, aCD5L:CD5L homodimer, and/or a CD5L:p40 heterodimer from binding to anIL-23 receptor; and/or (b) inhibits formation of the CD5L:CD5L homodimerand/or the CD5L:p40 heterodimer. In some embodiments, the agentcomprises an antibody, or an antigen binding fragment thereof, thatbinds to one or more of the CD5L, the CD5L homodimer, or the CD5L:p40heterodimer. In some embodiments, the agent comprises inhibitory nucleicacids that target the CD5L and/or the p40.

In some embodiments, the subject has cancer that is not inflammationrelated. Some embodiments comprise administering an anti-cancerimmunotherapy to the subject, such as checkpoint inhibitors, PD-1/PDL-1,anti-cancer vaccines, adoptive T cell therapy, and/or combination of twoor more thereof.

In embodiments that comprise administering inhibitory nucleic acids, thenucleic acids can include small interfering RNAs (e.g., shRNA),antisense oligonucleutides (e.g. antisense RNAs), and/or CRISPR-Cas.

In some embodiments, the subject has an immune deficiency, e.g., aprimary or secondary immune deficiency. In some embodiments, the subjecthas an infection with a pathogen, e.g., viral, bacterial, or fungalpathogen.

Some embodiments comprised methods of modulating CD8⁺ T cell exhaustionin a subject in need thereof, the method comprising administering to thesubject a therapeutically effective amount of an agent that: (a)inhibits CD5L, a CD5L:CD5L homodimer, and/or a CD5L:p40 heterodimer frombinding to an IL-23 receptor; and/or (b) inhibits formation of theCD5L:CD5L homodimer and/or the CD5L:p40 heterodimer. In someembodiments, said administering reduces CD8⁺ T cell exhaustion. In someembodiments the subject has cancer, such as a non-inflammatory cancer.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Methods and materials aredescribed herein for use in the present invention; other, suitablemethods and materials known in the art can also be used. The materials,methods, and examples are illustrative only and not intended to belimiting. All publications, patent applications, patents, sequences,database entries, and other references mentioned herein are incorporatedby reference in their entirety. In case of conflict, the presentspecification, including definitions, will control.

Other features and advantages of the invention will be apparent from thefollowing detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1. Soluble CD5L can regulate T cell function, largely reversingCD5L deficiency-induced gene expression pattern in T cells. WT orCD5L−/− naïve T cells were sorted and activated under Th0 condition andtreated with either PBS or soluble CD5L (50 nM). RNA was extracted at 96h and analyzed using nanostring platform using Th17 codesets of 312genes (only those showing a difference between any of the testedconditions were included in further analysis).

FIG. 2. Soluble CD5L (CD5Lm) and CD5L/p40 premix can have uniquefunctions on T cells. Similar to FIG. 1. Th0 cells were incubated withsoluble CD5L, CD5L/p40 mixture (premixed for 4 hours), p40 or controlPBS.

FIGS. 3A-C. The impact of soluble CD5L or CD5L/p40 can be dependent onIL-23R expression Similar to FIG. 1. CD5L−/− or CD5L−/− IL-23R−/− Th0cells were incubated with soluble CD5L, CD5L/p40 mixture (premixed for 4hours), p40 or control PBS.

FIGS. 4A-G CD5L regulates ILC function at steady state and duringinflammation. A-D. Naïve 6-month old mice that are either wildtype orCD5L^(−/−) were sacrificed and cells from tissues as indicated areanalyzed by flow cytometry or quantitative real time PCR. (A)IL-23R.GFP^(+/−) reporter mice that are otherwise wildtype or CD5L^(−/−)were used and cells were stained directly ex vivo; (B-C) Cells wereincubated with IL-7 or IL-7/CD5L overnight and restimulated withPMA/ionomycine in the presence of brefaldin A for four hours. Cells weresubsequently stained and analyzed by flow cytometry; (D) Cells wereanalyzed directly ex vivo by flow cytometry or sorted, RNA-extracted andanalyzed by real time qPCR; E-G. 6-8 wk old WT or CD5L^(−/−)IL-17^(Cre)Rosa26^(Td-tomato) mice were treated with 2.5% DSS indrinking water for 6 days followed by 5 days of regular water. Mice werethen sacrificed and cells isolated from respective tissues forPMA/ionomycine restimulation and flow cytometry analysis.

FIG. 5. CD5L and CD5L:p40 regulate CD11c⁺ DC function. CD11c⁺ cells wereenriched and sorted from spleen of WT, CD36−/− and IL-23R−/− naïve mice.CD11c+ cells were stimulated with 100 ng/ml LPS in the presence ofeither control, sCD5L, p40 or CD5L:p40 at 5 uM. Cells were harvested at24 hours.

FIGS. 6A-D. CD5L^(−/−) mice have more severe colitis in response toDSS-induced injury. 6-8 wk old WT or CD5L^(−/−) mice were treated with2.5% DSS in drinking water for 7 days followed by 7 days of regularwater. Weight (A), colitis score (B) and colon length (C) andrepresentative histology (D) were shown.

FIGS. 7A-D. Recombinant CD5L can bind to Th1 and Th17p (pathogenic Th17)cells and alleviate diseases severity of EAE and DSS induced colitis.Recombinant CD5L was generated with a His tag. A) Th0, Th1 (IL-12) andTh17p (IL-1b, IL-6, IL-23) are differentiated from naïve CD4 T cells invitro for 4 days and cells were harvested for staining with recombinantCD5L followed by anti-His APC antibodies and flow cytometry analysis. B)Wildtype (WT) mice were immunized with MOG/CFA followed by PT injectionto induce EAE. Mice at peak of disease (score=3) were injected witheither PBS (solid circles) or recombinant CD5L (empty circles, CD5Lm)intraperitoneally daily for five consecutive days and mice were followedfor disease progression. C) WT mice were induced with colitis with 2.5%DSS in drinking water for a consecutive of 6 days followed by normalwater for 8 days. Mice were given either control (PBS) or recombinantCD5L (CD5Lm) intraperitoneally on day 4, 6 and 8. Colon length andcolitis score are recorded on day 14.

FIGS. 8A-B. (A) Recombinant CD5L and CD5L:p40 (genetically linked) werecustom ordered from Biolegend. CD5L monomer formed a homodimer andCD5L:CD5L homodimer, which was further purified and was used insubsequent experiments to test its function separately; (B) Serum wascollected kinetically from WT and Cd5T mice with DSS-induced colitis (2%DSS in drinking water for 6 days followed by 7 days of normal water) andthe level of CD5L:p40 was measured using an ELISA developed in houseusing anti-p40 antibody for capturing, biotinylated anti-CD5L antibodyfor detection and recombinant CD5L:p40 as a positive control.

FIGS. 9A-B. FIG. 9A sets forth results of a screening assay showing thatTLR ligands can induce secretion of CD5L:p40. FIG. 9B sets forth flowcytometry experiments showing that IL-27 induces expression of CD5L.

FIGS. 10A-D. FIG. 10A sets forth results of FACS experiments showingthat CD5L homodimers and CD5L:p40 heterodimers inhibit IL-17 expressionin pathogenic Th17 cells; FIG. 10(B) shows results of an serum ELISAmeasurements showing that both forms of CD5L inhibit IL-17 expression;FIGS. 10C and D show cell signatures for pathogenic Th17 cells treatedwith CD5L homodimers and CD5L:p40 heterodimers, respectively.

FIGS. 11A-B. FIG. 11A shows inhibited IL-27 expression in pathogenicTh17 cells treated with CD5L homodimers and CD5L:p40 heterodimers, asmeasured by ELISA and qPCR; FIG. 11B shows that IFNg expression in Th1cells is inhibited by CD5L:CD5L homodimer and CD5L:p40 heterodimer, asmeasured by flow cytometry analysis.

FIGS. 12A-B. FIGS. 12A and B show heat maps and GSEA analysis for Th17cells and Th1 cells, respectively, following treatment with CD5Lhomodimers and CD5L:p40 heterodimers.

FIGS. 13A-B. FIG. 13A compares EAE disease severity measurements inwildtype mice and CD5L knockout mice; FIG. 13B compares CD5L expressionlevels in Th17 and macrophage cells in the spleen and CNS.

FIGS. 14A-B. FIG. 14A shows a construct used to generate CD5Lconditional knockout mice; FIG. 14B shows that mice CD5L deletion micewere produced in myeloid lineage cells, T cells, and IL-17 producingcells.

FIG. 15A-B. FIG. 15A sets forth a plot demonstrating tumor growth inCD5L^(flox/flox)Lymz^(Cre+) mice injected with colon carcinoma; FIG. 15Bsets forth pictures showing tumor size in CD50L^(flox/flox) mice andCD5L knockout mice 19 days after tumor injection.

FIG. 16. FIG. 16 depicts the lipodome of wildtype and cd5l^(−/−) Th17cells differentiated under pathogenic and non-pathogenic conditions.

FIG. 17. FIG. 17 is a plot showing that metabolic transcriptomeexpression covaries with Th17 cell pathogenicity.

FIGS. 18A-D. FIG. 18 sets forth plots showing suppression of tumorprogression in CD5L^(−/−) mice injected with MC38 (FIG. 19A) andMC38-OVA (FIG. 19B) colon carcinoma; FIGS. 18C and D set forth flowcytometry diagrams assessing tumor infiltrating lymphocytes andcytokines, respectively, in CD5L^(−/−) mice and control mice.

FIGS. 19A-B. FIG. 19 sets forth graphs showing CD5L:CD5L homodimerexpression (FIG. 19A) and CD5L:p40 heterodimer expression (FIG. 19B) inserum during tumor progression, as measured using ELISA assays.

FIG. 20. FIG. 20 sets forth a heat map showing differentially expressedgenes in CD5L:CD5L and CD5L:p40 experiments as compared to the control(differentially expressed genes are defined by p<0.5 as compared tocontrol).

FIGS. 21A-B. FIGS. 21A-B set forth data showing the impact of CD5L:p40and CD5L:CD5L on Tregs in vivo in DSS-induced colitis; FIG. 21A showsfrequency of Foxp3+ CD4 T cells in cells from mesenteric lymph node(mLN), peyer's patches (pp), lamina propria of colon (LP), andintraepithelial lymphocytes (IEL); FIG. 21B sets forth data showing thatCD5L:p40 decreased ILC3 in lamina propria cells.

FIGS. 22A-B. FIG. 22A sets forth data showing serum concentrations ofCD5L:p40 and CD5L:CD5L in mice immunized with CD5L:p40 and CD5L:CD5L,respectively; FIG. 22B sets forth data showing pools of antibodiesspecific to either CD5L:p40 or CD5L:CD5L, and which were obtained frommice immunized with CD5L:p40 and CD5L:CD5L, respectively.

FIGS. 23A-D. FIG. 23 demonstrates homology between mice and humanprotein sequences for CD5L (FIG. 23A), p19 (FIG. 23B), p40 (FIG. 23C),and p35 (FIG. 23D).

DETAILED DESCRIPTION

Interleukin 23 (IL-23) is formed of a heterodimer by p19 and p40. p40,also known as interleukin 12B, can form heterodimers with two othercytokines: p35 to make IL-12 and potentially CD5 Antigen Like protein(CD5L) (also known as apoptosis inhibitor of macrophage (AIM), SP-a, andApi6) to make CD5L:p40. It has not previously been demonstrated that theCD5L:p40 dimer has any function. Th17-cell intrinsic CD5L can regulateTh17 cell pathogenicity and regulate IL-23R expression (seeWO2015130968). CD5L is a secreted protein and it may form a heterodimerwith p40 (Abdi et al., 2014). Applicants tested the hypothesis thatsoluble CD5L, as a monomer, homodimer, or heterodimer with p40, canfunction as a cytokine regulating T cell function. Surprisingly,Applicants found that soluble CD5L, CD5L:CD5L homodimer, and CD5L:p40heterodimer share a distinct ability to regulate T cell function. Not tobe bound by theory, CD5L, either as a monomer, homodimer, or aheterodimer, is suspected to interfere with the pathogenic andnon-pathogenic program of Th17 cells. Such findings have therapeuticimplications with respect to neuroinflammation, autoimmune disorders,inflammatory cancers, and non-inflammatory cancers and disorders, interalia.

CD5L function is largely dependent not on CD36, the known receptor forCD5L, but IL-23R expression on T cells. Further, CD5L:p40 appears to beless dependent on IL-23R and may require a different receptor forsignaling. Moreover, CD5L can regulate not only T cells, but also otherIL-23R expressing cells such as innate lymphoid cells and dendriticcells. CD5L plays a critical role in protecting host from acuteinflammation and potentially tumor progression.

CD5L Proteins and CD5L:p40 Heterodimers

In some embodiments, the methods described herein can include theadministration of soluble CD5L, CD5L:CD5L homodimers, or CD5L:p40heterodimers. The homodimers include CD5L complexed to another CD5L,preferably complexed together in a homodimeric form. The heterodimersinclude p40 protein and CD5L protein, preferably complexed together in aheterodimeric form. The protein sequences will preferably be chosenbased on the species of the recipient; thus, for example, human p40and/or human CD5L can be used to treat a human subject. The sequences ofhuman p40 and CD5L are as follows:

Human p40 (interleukin-12 subunit beta) precursor (SEQ ID NO: 1)   1mchqqlvisw fslvflaspl vaiwelkkdv yvveldwypd apgemvvltc dtpeedgitw  61tldqssevlg sgktltiqvk efgdaggytc hkggevlshs llllhkkedg iwstdilkdq 121kepknktflr ceaknysgrf tcwwlttist dltfsvkssr gssdpqgvtc gaatlsaerv 181rgdnkeyeys vecqedsacp aaeeslpiev mvdavhklky enytssffir diikpdppkn 241lqlkplknsr qvevsweypd twstphsyfs ltfcvqvqgk skrekkdrvf tdktsatvic 301rknasisvra qdryysssws ewasvpcsIn some embodiments, amino acids 23-328 of SEQ ID NO:1 (leaving off thesignal sequence) are used. An exemplary mRNA sequence encoding p40 isaccessible in GenBank at No. NM_002187.2.

CD5 molecule-like (CD5L) (SEQ ID NO: 2)   1mallfslila ictrpgflas psgvrlvggl hrcegrveve qkgqwgtvcd dgwdikdvav  61lcrelgcgaa sgtpsgilye ppaekeqkvl igsVsctgte dtlagcegee vydcshdeda 121gascenpess fspvpegvrl adgpghckgr vevkhqnqwy tvcqtgwslr aakvvcrqlg 181cgravltqkr cnkhaygrkp iwlsqmscsg reatlqdcps gpwgkntcnh dedtwveced 241pfdlrlvggd nlcsgrlevl hkgvwgsvcd dnwgekedqv vckqlgcgks lspsfrdrkc 301ygpgvgriwl dnvrcsgeeq sleqcqhrfw gfhdcthqed vavicsgIn some embodiments, amino acids 20-347 of SEQ ID NO:2 (leaving off thesignal sequence) are used. An exemplary mRNA sequence encoding CD5L isaccessible in GenBank at No. NM_005894.2.

Methods for making recombinant proteins are well known in the art,including in vitro translation and expression in a suitable host cellfrom nucleic acid encoding the variant protein. A number of methods areknown in the art for producing proteins. For example, the proteins canbe produced in and purified from yeast, E. coli, insect cell lines,plants, transgenic animals, or cultured mammalian cells; see, e.g.,Palomares et al., “Production of Recombinant Proteins: Challenges andSolutions,” Methods Mol Biol. 2004; 267:15-52. In some embodiments,recombinant p40 and CD5L proteins are obtained and mixed in roughlyequimolar amounts of p40 with CD5L and incubated, e.g., at 37° C.Immunoprecipitation and purification can be used to confirm formation ofheterodimers, as can size exclusion chromatography or other purificationmethods, to obtain a substantially pure population of heterodimers. Insome embodiments, p40 and CD5L are simply mixed together underconditions sufficient for heterodimerization, and optionally purified toobtain a substantially pure composition of heterodimers; alternatively,the heterodimers can be cross-linked and then purified. In someembodiments, an agent such as TLR9 can be used to increase heterodimerformation, e.g., in vitro or in vivo.

In some embodiments, the methods include administering nucleic acidsencoding a p40 and/or CD5L polypeptides or active fragment thereof. Insome embodiments, the nucleic acids are incorporated into a geneconstruct to be used as a part of a gene therapy or cell therapyprotocol. In some embodiments, the methods include targeted expressionvectors for transfection and expression of polynucleotides that encodep40 and/or CD5L polypeptides as described herein, in particular celltypes, especially in T cells. Expression constructs of such componentscan be administered in any effective carrier, e.g., any formulation orcomposition capable of effectively delivering the component gene tocells in vivo. Approaches include insertion of the gene in viralvectors, including recombinant retroviruses, adenovirus,adeno-associated virus, lentivirus, and herpes simplex virus-1, orrecombinant bacterial or eukaryotic plasmids. Viral vectors transfectcells directly; plasmid DNA can be delivered naked or with the help of,for example, cationic liposomes (lipofectamine) or derivatizedconjugates (e.g., antibody conjugated), polylysine conjugates,gramacidin S, artificial viral envelopes or other such intracellularcarriers, as well as direct injection of the gene construct or CaPO₄precipitation carried out in vivo.

A preferred approach for in vivo introduction of nucleic acid into acell is by use of a viral vector containing nucleic acid, e.g., a cDNA.Infection of cells with a viral vector has the advantage that a largeproportion of the targeted cells can receive the nucleic acid.Additionally, molecules encoded within the viral vector, e.g., by a cDNAcontained in the viral vector, are expressed efficiently in cells thathave taken up viral vector nucleic acid.

Retrovirus vectors and adeno-associated virus vectors can be used as arecombinant gene delivery system for the transfer of exogenous genes invivo, particularly into humans. These vectors provide efficient deliveryof genes into cells, and the transferred nucleic acids are stablyintegrated into the chromosomal DNA of the host. The development ofspecialized cell lines (termed “packaging cells”) which produce onlyreplication-defective retroviruses has increased the utility ofretroviruses for gene therapy, and defective retroviruses arecharacterized for use in gene transfer for gene therapy purposes (for areview see Miller, Blood 76:271 (1990)). A replication defectiveretrovirus can be packaged into virions, which can be used to infect atarget cell through the use of a helper virus by standard techniques.Protocols for producing recombinant retroviruses and for infecting cellsin vitro or in vivo with such viruses can be found in Ausubel, et al.,eds., Current Protocols in Molecular Biology, Greene PublishingAssociates, (1989), Sections 9.10-9.14, and other standard laboratorymanuals. Examples of suitable retroviruses include pLJ, pZIP, pWE andpEM which are known to those skilled in the art. Examples of suitablepackaging virus lines for preparing both ecotropic and amphotropicretroviral systems include ΨCrip, ΨCre, Ψ2 and ΨAm. Retroviruses havebeen used to introduce a variety of genes into many different celltypes, including epithelial cells, in vitro and/or in vivo (see forexample Eglitis, et al. (1985) Science 230:1395-1398; Danos and Mulligan(1988) Proc. Natl. Acad. Sci. USA 85:6460-6464; Wilson et al. (1988)Proc. Natl. Acad. Sci. USA 85:3014-3018; Armentano et al. (1990) Proc.Natl. Acad. Sci. USA 87:6141-6145; Huber et al. (1991) Proc. Natl. Acad.Sci. USA 88:8039-8043; Ferry et al. (1991) Proc. Natl. Acad. Sci. USA88:8377-8381; Chowdhury et al. (1991) Science 254:1802-1805; vanBeusechem et al. (1992) Proc. Natl. Acad. Sci. USA 89:7640-7644; Kay etal. (1992) Human Gene Therapy 3:641-647; Dai et al. (1992) Proc. Natl.Acad. Sci. USA 89:10892-10895; Hwu et al. (1993) J. Immunol.150:4104-4115; U.S. Pat. No. 4,868,116; U.S. Pat. No. 4,980,286; PCTApplication WO 89/07136; PCT Application WO 89/02468; PCT Application WO89/05345; and PCT Application WO 92/07573).

Another viral gene delivery system useful in the present methodsutilizes adenovirus-derived vectors. The genome of an adenovirus can bemanipulated, such that it encodes and expresses a gene product ofinterest but is inactivated in terms of its ability to replicate in anormal lytic viral life cycle. See, for example, Berkner et al.,BioTechniques 6:616 (1988); Rosenfeld et al., Science 252:431-434(1991); and Rosenfeld et al., Cell 68:143-155 (1992). Suitableadenoviral vectors derived from the adenovirus strain Ad type 5 dl324 orother strains of adenovirus (e.g., Ad2, Ad3, or Ad7 etc.) are known tothose skilled in the art. Recombinant adenoviruses can be advantageousin certain circumstances, in that they are not capable of infectingnon-dividing cells and can be used to infect a wide variety of celltypes, including epithelial cells (Rosenfeld et al., (1992) supra).Furthermore, the virus particle is relatively stable and amenable topurification and concentration, and as above, can be modified so as toaffect the spectrum of infectivity. Additionally, introduced adenoviralDNA (and foreign DNA contained therein) is not integrated into thegenome of a host cell but remains episomal, thereby avoiding potentialproblems that can occur as a result of insertional mutagenesis in situ,where introduced DNA becomes integrated into the host genome (e.g.,retroviral DNA). Moreover, the carrying capacity of the adenoviralgenome for foreign DNA is large (up to 8 kilobases) relative to othergene delivery vectors (Berkner et al., supra; Haj-Ahmand and Graham, J.Virol. 57:267 (1986)).

Yet another viral vector system useful for delivery of nucleic acids isthe adeno-associated virus (AAV). Adeno-associated virus is a naturallyoccurring defective virus that requires another virus, such as anadenovirus or a herpes virus, as a helper virus for efficientreplication and a productive life cycle. (For a review see Muzyczka etal., Curr. Topics in Micro. and Immunol. 158:97-129 (1992)). It is alsoone of the few viruses that may integrate its DNA into non-dividingcells, and exhibits a high frequency of stable integration (see forexample Flotte et al., Am. J. Respir. Cell. Mol. Biol. 7:349-356 (1992);Samulski et al., J. Virol. 63:3822-3828 (1989); and McLaughlin et al.,J. Virol. 62:1963-1973 (1989)). Vectors containing as little as 300 basepairs of AAV can be packaged and can integrate. Space for exogenous DNAis limited to about 4.5 kb. An AAV vector such as that described inTratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985) can be used tointroduce DNA into cells. A variety of nucleic acids have beenintroduced into different cell types using AAV vectors (see for exampleHermonat et al., Proc. Natl. Acad. Sci. USA 81:6466-6470 (1984);Tratschin et al., Mol. Cell. Biol. 4:2072-2081 (1985); Wondisford etal., Mol. Endocrinol. 2:32-39 (1988); Tratschin et al., J. Virol.51:611-619 (1984); and Flotte et al., J. Biol. Chem. 268:3781-3790(1993)).

In addition to viral transfer methods, such as those illustrated above,non-viral methods can also be employed to cause expression of a nucleicacid compound described herein (e.g., nucleic acids encoding p40 and/orCD5L polypeptides) in the tissue of a subject. Typically non-viralmethods of gene transfer rely on the normal mechanisms used by mammaliancells for the uptake and intracellular transport of macromolecules. Insome embodiments, non-viral gene delivery systems can rely on endocyticpathways for the uptake of the subject gene by the targeted cell.Exemplary gene delivery systems of this type include liposomal derivedsystems, poly-lysine conjugates, and artificial viral envelopes. Otherembodiments include plasmid injection systems such as are described inMeuli et al., J. Invest. Dermatol. 116(1):131-135 (2001); Cohen et al.,Gene Ther. 7(22):1896-905 (2000); or Tam et al., Gene Ther.7(21):1867-74 (2000).

In some embodiments, genes encoding p40 and/or CD5L polypeptides areentrapped in liposomes bearing positive charges on their surface (e.g.,lipofectins), which can be tagged with antibodies against cell surfaceantigens of the target tissue (see, e.g., Mizuno et al., No Shinkei Geka20:547-551 (1992); PCT publication WO91/06309; Japanese patentapplication 1047381; and European patent publication EP-A-43075)).

In clinical settings, the gene delivery systems for the therapeutic genecan be introduced into a subject by any of a number of methods, each ofwhich is familiar in the art. For instance, a pharmaceutical preparationof the gene delivery system can be introduced systemically, e.g., byintravenous injection, and specific transduction of the protein in thetarget cells will occur predominantly from specificity of transfection,provided by the gene delivery vehicle, cell-type or tissue-typeexpression due to the transcriptional regulatory sequences controllingexpression of the receptor gene, or a combination thereof. In otherembodiments, initial delivery of the recombinant gene is more limited,with introduction into the subject being quite localized. For example,the gene delivery vehicle can be introduced by catheter (see U.S. Pat.No. 5,328,470) or by stereotactic injection (e.g., Chen et al., PNAS USA91: 3054-3057 (1994)).

The pharmaceutical preparation of the gene therapy construct can consistessentially of the gene delivery system in an acceptable diluent, or cancomprise a slow release matrix in which the gene delivery vehicle isembedded. Alternatively, where the complete gene delivery system can beproduced intact from recombinant cells, e.g., retroviral vectors, thepharmaceutical preparation can comprise one or more cells, which producethe gene delivery system.

Pharmaceutical Compositions

The methods described herein include the manufacture and use ofpharmaceutical compositions, which include an agent described herein asactive ingredient(s). Also included are the pharmaceutical compositionsthemselves.

Pharmaceutical compositions typically include a pharmaceuticallyacceptable carrier. As used herein the language “pharmaceuticallyacceptable carrier” includes saline, solvents, dispersion media,coatings, antibacterial and antifungal agents, isotonic and absorptiondelaying agents, and the like, and combinations of two or more thereof,compatible with pharmaceutical administration. Supplementary activecompounds can also be incorporated into the compositions.

Pharmaceutical compositions are typically formulated to be compatiblewith the intended route of administration. Examples of routes ofadministration that are especially useful in the present methods includeparenteral (e.g., intravenous), intrathecal, oral, and nasal orintranasal (e.g., by administration as drops or inhalation)administration. In some embodiments, such as for compounds that don'tcross the blood brain barrier, delivery directly into the CNS or CSF canbe used, e.g., using implanted intrathecal pumps (see, e.g., Borrini etal., Archives of Physical Medicine and Rehabilitation 2014; 95:1032-8;Penn et al., N. Eng. J. Med. 320:1517-21 (1989); and Rezai et al., PainPhysician 2013; 16:415-417) or nanoparticles, e.g., gold nanoparticles(e.g., glucose-coated gold nanoparticles, see, e.g., Gromnicova et al.(2013) PLoS ONE 8(12): e81043). Methods of formulating and deliveringsuitable pharmaceutical compositions are known in the art, see, e.g.,the books in the series Drugs and the Pharmaceutical Sciences: a Seriesof Textbooks and Monographs (Dekker, N.Y.); and Allen et al., Ansel'sPharmaceutical Dosage Forms and Drug Delivery Systems, LippincottWilliams & Wilkins; 8th edition (2004).

Pharmaceutical compositions suitable for injectable use can includesterile aqueous solutions (where water soluble) or dispersions andsterile powders for the extemporaneous preparation of sterile injectablesolutions or dispersion. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringability exists. It should be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyetheylene glycol, and the like), and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousantibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in thecomposition. Prolonged absorption of the injectable compositions can bebrought about by including in the composition an agent that delaysabsorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the activecompound in the required amount in an appropriate solvent with one or acombination of ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the active compound into a sterile vehicle, which containsa basic dispersion medium and the required other ingredients from thoseenumerated above. In the case of sterile powders for the preparation ofsterile injectable solutions, the preferred methods of preparation arevacuum drying and freeze-drying, which yield a powder of the activeingredient plus any additional desired ingredient from a previouslysterile-filtered solution thereof.

For oral administration, the compositions can be formulated with aninert diluent or an edible carrier. For the purpose of oral therapeuticadministration, the active compound can be incorporated with excipientsand used in the form of tablets, troches, or capsules, e.g., gelatincapsules. Oral compositions can also be prepared using a fluid carrierfor use as a mouthwash. Pharmaceutically compatible binding agents,and/or adjuvant materials can be included as part of the composition.The tablets, pills, capsules, troches and the like can contain any ofthe following ingredients, or compounds of a similar nature: a bindersuch as microcrystalline cellulose, gum tragacanth or gelatin; anexcipient such as starch or lactose, a disintegrating agent such asalginic acid, Primogel, or corn starch; a lubricant such as magnesiumstearate or Sterotes; a glidant such as colloidal silicon dioxide; asweetening agent such as sucrose or saccharin; or a flavoring agent suchas peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds can be delivered in theform of an aerosol spray from a pressured container or dispenser thatcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer. Such methods include those described in U.S. Pat. No.6,468,798.

Therapeutic compounds that are or include nucleic acids can beadministered by any method suitable for administration of nucleic acidagents, such as a DNA vaccine. These methods include gene guns, bioinjectors, and skin patches as well as needle-free methods such as themicro-particle DNA vaccine technology disclosed in U.S. Pat. No.6,194,389, and the mammalian transdermal needle-free vaccination withpowder-form vaccine as disclosed in U.S. Pat. No. 6,168,587.Additionally, intranasal delivery is possible, as described in, interalia, Hamajima et al., Clin. Immunol. Immunopathol., 88(2), 205-10(1998).

Liposomes (e.g., as described in U.S. Pat. No. 6,472,375) andmicroencapsulation can also be used to deliver a compound describedherein. Biodegradable microparticle delivery systems can also be used(e.g., as described in U.S. Pat. No. 6,471,996).

In one embodiment, the therapeutic compounds are prepared with carriersthat will protect the therapeutic compounds against rapid eliminationfrom the body, such as a controlled release formulation, includingimplants and microencapsulated delivery systems. Biodegradable,biocompatible polymers can be used, such as ethylene vinyl acetate,polyanhydrides, polyglycolic acid, collagen, polyorthoesters, andpolylactic acid. Such formulations can be prepared using standardtechniques, or obtained commercially, e.g., from Alza Corporation andNova Pharmaceuticals, Inc. Liposomal suspensions (including liposomestargeted to selected cells with monoclonal antibodies to cellularantigens) can also be used as pharmaceutically acceptable carriers.These can be prepared according to methods known to those skilled in theart, for example, as described in U.S. Pat. No. 4,522,811.

The pharmaceutical compositions can be included in a container, pack, ordispenser, e.g., single-dose dispenser together with instructions foradministration. The container, pack, or dispenser can also be includedas part of a kit that can include, for example, sufficient single-dosedispensers for one day, one week, or one month of treatment.

Dosage

Dosage, toxicity and therapeutic efficacy of the compounds can bedetermined, e.g., by standard pharmaceutical procedures in cell culturesor experimental animals, e.g., for determining the LD50 (the dose lethalto 50% of the population) and the ED50 (the dose therapeuticallyeffective in 50% of the population). The dose ratio between toxic andtherapeutic effects is the therapeutic index and it can be expressed asthe ratio LD50/ED50. Compounds that exhibit high therapeutic indices arepreferred. While compounds that exhibit toxic side effects may be used,care should be taken to design a delivery system that targets suchcompounds to the site of affected tissue in order to minimize potentialdamage to uninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch compounds lies preferably within a range of circulatingconcentrations that include the ED50 with little or no toxicity. Thedosage may vary within this range depending upon the dosage formemployed and the route of administration utilized. For any compound usedin the method of the invention, the therapeutically effective dose canbe estimated initially from cell culture assays. A dose may beformulated in animal models to achieve a circulating plasmaconcentration range that includes the IC50 (i.e., the concentration ofthe test compound that achieves a half-maximal inhibition of symptoms)as determined in cell culture. Such information can be used to moreaccurately determine useful doses in humans. Levels in plasma may bemeasured, for example, by high performance liquid chromatography.

An “effective amount” is an amount sufficient to effect beneficial ordesired results. For example, a therapeutic amount is one that achievesthe desired therapeutic effect. This amount can be the same or differentfrom a prophylactically effective amount, which is an amount necessaryto prevent onset of disease or disease symptoms. An effective amount canbe administered in one or more administrations, applications or dosages.A therapeutically effective amount of a composition depends on thecomposition selected. The compositions can be administered one from oneor more times per day to one or more times per week; including onceevery other day. The skilled artisan will appreciate that certainfactors may influence the dosage and timing required to effectivelytreat a subject, including but not limited to the severity of thedisease or disorder, previous treatments, the general health and/or ageof the subject, and other diseases present. Moreover, treatment of asubject with a therapeutically effective amount of the compositionsdescribed herein can include a single treatment or a series oftreatments.

Methods of Treatment—Decreasing Immune Responses

Without being bound by theory, CD5L monomers, homodimers andheterodimers with p40 are believed to regulate T cells and alter immunefunction, and can promote suppression of pathogenic Th17 and Th1phenotypes. Agonists of CD5L, CD5L:CD5L homodimers, and/or CD5L:p40heterodimers (e.g., CD5L:p40 heterodimer polypeptides), can beadministered to treat conditions associated with overactive inflammationor immunity, e.g., autoimmune diseases, e.g., in which pathogenic Tcells are present at increased levels and/or have increased activity,such as multiple sclerosis (MS). Autoimmune conditions that may benefitfrom treatment using the compositions and methods described hereininclude, but are not limited to, for example, MS, Addison's Disease,alopecia, ankylosing spondylitis, antiphospholipid syndrome, autoimmunehemolytic anemia, autoimmune hepatitis, autoimmune oophoritis, Bechet'sdisease, bullous pemphigoid, celiac disease, chronic fatigue immunedysfunction syndrome (CFIDS), chronic inflammatory demyelinatingpolyneuropathy, Churg-Strauss syndrome, cicatricial pemphigoid, coldagglutinin disease, CREST Syndrome, Crohn's disease, diabetes (e.g.,type I), dysautonomia, endometriosis, eosinophilia-myalgia syndrome,essential mixed cryoglobulinemia, fibromyalgia, syndrome/fibromyositis,Graves' disease, Guillain Barré syndrome, Hashimoto's thyroiditis,idiopathic pulmonary fibrosis, idiopathic thrombocytopenia purpura(ITP), inflammatory bowel disease (IBD), lichen planus, lupus, Ménière'sdisease, mixed connective tissue disease (MCTD), multiple sclerosis,myasthenia gravis, pemphigus, pernicious anemia, polyarteritis nodosa,polychondritis, polymyalgia rheumatica, polymyositis anddermatomyositis, primary agammaglobulinemia, primary biliary cirrhosis,psoriasis, Raynaud's phenomenon, Reiter's syndrome, rheumatic fever,rheumatoid arthritis, sarcoidosis, scleroderma, Sjögren's syndrome,spondyloarthropathy (spondyloarthritides), stiff-man syndrome, Takayasuarteritis, temporal arteritis/giant cell arteritis, autoimmune thyroiddisease, ulcerative colitis, autoimmune uveitis, autoimmune vasculitis,vitiligo, and Wegener's granulomatosis. In some embodiments, theautoimmune disease is MS, IBD, Crohn's disease, spondyloarthritides,Systemic Lupus Erythematosus, Vitiligo, rheumatoid arthritis, psoriasis,Sjögren's syndrome, or diabetes, e.g., Type I diabetes, all of whichhave been linked to Th17 cell dysfunction (see, e.g., Korn et al., AnnuRev Immunol. 2009; 27:485-517Dong, Cell Research (2014) 24:901-903;Zambrano-Zaragoza et al., Int J Inflam. 2014; 2014: 651503; Waite andSkokos, International Journal of Inflammation; Volume 2012 (2012),Article ID 819467, 10 pages, dx.doi.org/10.1155/2012/819467; Han et al.,Frontiers of Medicine 9(1):10-19 (2015).

Some embodiments include treatment of autoimmune diseases, such asmultiple sclerosis (MS) or IBD, using CD5L monomers, CD5L homodimersand/or CD5L:p40 heterodimers. In some embodiments, once it has beendetermined that a person has an autoimmune disease, e.g., MS or IBD,then a treatment comprising administration of a therapeuticallyeffective amount of CD5L monomers, CD5L homodimers and/or CD5L:p40heterodimers can be administered.

Generally, the methods include administering a therapeutically effectiveamount of CD5L monomers, CD5L homodimers and/or CD5L:p40 heterodimers asdescribed herein, to a subject who is in need of, or who has beendetermined to be in need of, such treatment. As used in this context, to“treat” means to ameliorate or reduce the severity of at least onesymptom of a disease or condition. For instance, a treatment can resultin a reduction in one or more symptoms of an autoimmune disease, e.g.,for MS, e.g., depression and fatigue, bladder dysfunction, spasticity,pain, ataxia, and intention tremor. A therapeutically effective amountcan be an amount sufficient to prevent the onset of an acute episode orto shorten the duration of an acute episode, or to decrease the severityof one or more symptoms, e.g., heat sensitivity, internuclearophthalmoplegia, optic neuritis, and Lhermitte symptom. In someembodiments, a therapeutically effective amount is an amount sufficientto prevent the appearance of, delay or prevent the growth (i.e.,increase in size) of, or promote the healing of a demyelinated lesion inone or more of the brain, optic nerves, and spinal cord of the subject,e.g., as demonstrated on MRI.

Alternatively or in addition, the methods can be used to treat otherconditions associated with hyperimmune responses, e.g., cancersassociated with inflammation such as colorectal cancers. In certaininflammation-related cancers the IL-23 pathway has been shown to promotetumorigenesis (e.g., in colorectal cancer, carcinogen-induced skinpapilloma, fibrosarcomas, mammary carcinomas and certain cancermetastasis; these studies have suggested that IL-23 and Th17 cells playa role in some cancers, such as, by way of non-limiting example,colorectal cancers. See e.g., Ye J, Livergood R S, Peng G. “The role andregulation of human Th17 cells in tumor immunity.” Am J Pathol 2013January; 182(1): 10-20. doi: 10.1016/j.ajpath.2012.08.041. Epub 2012Nov. 14). In such cancer types, CD5L and CD5L:p40 and agents thatpromote their function can have anti-tumor effects. (Teng et al., 2015Nat Med 21; Wang and Karin, Clin Exp Rheumatol 2015; 33). Thus CD5Lmonomers, CD5L homodimers and/or CD5L:p40 heterodimers, or nucleic acidsencoding CD5L monomers, CD5L homodimers and/or CD5L:p40 heterodimers,can be used to treat or reduce risk of developing these cancers.

Standard Treatments for Autoimmune Disease

In some embodiments, a treatment, e.g., comprising CD5L, CD5L:CD5Lhomodimers, or CD5L:p40 heterodimers, is administered in combinationwith a standard treatment for an autoimmune disease. For example, in thecase of MS, treatment can include administration of corticosteroidtherapy, interferon beta-1b, Glatiramer acetate, mitoxantrone,Fingolimod, teriflunomide, dimethyl fumarate, natalizumab, cannabis, ora combination thereof. In some embodiments, the treatment describedherein is administered in combination with a treatment for one or moresymptoms of MS, e.g., depression and/or fatigue, bladder dysfunction,spasticity, pain, ataxia, and intention tremor. Such treatments caninclude pharmacological agents, exercise, and/or appropriate orthotics.Additional information on the diagnosis and treatment of MS can be foundat the National MS Society website, on the world wide web atnationalmssociety.org.

Methods of Treatment—Enhancing Immune Responses

As shown herein and noted above, CD5L, CD5L:CD5L, and/or CD5L:p40 canregulate T cells and alter immune function. Methods that decrease thelevels or activity of this CD5L, the CD5L homodimer, and/or the CD5L:p40heterodimer can also be used to increase immune responses, e.g., totreat: subjects who have cancers that would benefit from immunotherapy(e.g., cancers that are not inflammation related); subjects who have aprimary or secondary immune deficiency; or subjects who have aninfection with a pathogen, e.g., viral, bacterial, or fungal pathogen.

Some embodiments comprised methods of modulating CD8⁺ T cell exhaustion,e.g., by administering a therapeutically effective amount of an agentthat: (a) inhibits CD5L, a CD5L:CD5L homodimer, and/or a CD5L:p40heterodimer from binding to an IL-23 receptor; and/or (b) inhibitsformation of the CD5L:CD5L homodimer and/or the CD5L:p40 heterodimer.Some embodiments comprise reducing CD8⁺ T cell exhaustion ordysfunction. Some embodiments comprise increasing CD8⁺ T cell activity.

In some embodiments, the methods include administering an agent thatspecifically inhibits binding of the CD5L monomer, CD5L homodimer,and/or CD5L:p40 heterodimer to a cognate receptor (e.g., the IL-23receptor or the IL-12 receptor, beta 1 subunit), or that specificallyinhibits formation of the CD5L homodimer or CD5L:p40 heterodimer. Insome embodiments, the agent is an antibody, or an antigen bindingfragment thereof, that binds to and inhibits the activity of the CD5Lmonomer, CD5L homodimer, and/or CD5L:p40 heterodimer. In someembodiments, the agent is an antagonist of CD5L, CD5L:CD5L homodimer, orCD5L:p40 heterodimer. In some embodiments, the methods includeinhibiting expression of CD5L and/or p40, for example using CRISPR or byadministering inhibitory nucleic acids that inhibit expression of CD5Land/or p40.

As used in this context, to “treat” means to ameliorate or reduce theseverity of at least one clinical parameter of the cancer. In someembodiments, the parameter is tumor size, tumor growth rate, recurrence,or metastasis, and an improvement would be a reduction in tumor size orno change in a normally fast growing tumor; a reduction or cessation oftumor growth; a reduction in, delayed, or no recurrence, or a reductionin, delayed, or no metastasis. Administration of a therapeuticallyeffective amount of a compound described herein for the treatment of acancer would result in one or more of a reduction in tumor size or nochange in a normally fast growing tumor; a reduction or cessation oftumor growth; or a reduction in, delayed, or no metastasis. In someembodiments, e.g., a treatment designed to prevent recurrence of cancer,the treatment would be given after a localized tumor has been removed,e.g., surgically, or treated with radiation therapy or with targetedtherapy with or without other therapies such as standard chemotherapy.Without wishing to be bound by theory, such a treatment may work bykeeping micrometastases dormant, e.g., by preventing them from beingreleased from dormancy.

As used herein, the term “hyperproliferative” refer to cells having thecapacity for autonomous growth, i.e., an abnormal state or conditioncharacterized by rapidly proliferating cell growth. Hyperproliferativedisease states may be categorized as pathologic, i.e., characterizing orconstituting a disease state, or may be categorized as non-pathologic,i.e., a deviation from normal but not associated with a disease state.The term is meant to include all types of cancerous growths or oncogenicprocesses, metastatic tissues or malignantly transformed cells, tissues,or organs, irrespective of histopathologic type or stage ofinvasiveness. A “tumor” is an abnormal growth of hyperproliferativecells. “Cancer” refers to pathologic disease states, e.g., characterizedby malignant tumor growth. The methods described herein can be used totreat cancer, e.g., solid tumors of epithelial origin, e.g., as definedby the ICD-O (International Classification of Diseases—Oncology) code(revision 3), section (8010-8790), e.g., early stage cancer, isassociated with the presence of a massive levels of satellite due toincrease in transcription and processing of satellite repeats inepithelial cancer cells. Thus the methods can include the interferenceof satellite repeats in a sample comprising cells known or suspected ofbeing tumor cells, e.g., cells from solid tumors of epithelial origin,e.g., pancreatic, lung, breast, prostate, renal, ovarian orcolon/colorectal cancer cells.

Cancers of epithelial origin can include pancreatic cancer (e.g.,pancreatic adenocarcinoma), lung cancer (e.g., non-small cell lungcarcinoma or small cell lung carcinoma), prostate cancer, breast cancer,renal cancer, ovarian cancer, melanoma or colon cancer. Leukemia mayinclude AML, CML or CLL and in some embodiments comprises cancerousMDSC. The methods can also be used to treat early preneoplastic cancersas a means to prevent the development of invasive cancer.

In some embodiments, CD5L, CD5L homodimer, and/or CD5L:p40 heterodimermay be used as a biomarker for cancer progression. For example, serumCD5L, CD5L homodimer, and/or CD5L:p40 concentration can be measured andcompared against a control concentration. In some embodiments, serumCD5L, CD5L homodimer, and/or CD5L:p40 concentration in a subject ismeasured at multiple time points, and the change in concentration isused to indicate progression of the cancer.

Standard Treatments for Cancer

In some embodiments, the methods include administering a standardanti-cancer therapy to a subject. Cancer treatments include those knownin the art, e.g., surgical resection with cold instruments or lasers,radiotherapy, phototherapy, biologic therapy (e.g., with tyrosine kinaseinhibitors), radiofrequency ablation (RFA), radioembolisation (e.g.,with 90^(Y) spheres), chemotherapy, and immunotherapy. Immunotherapiescan also include administering one or more of: adoptive cell transfer(ACT) involving transfer of ex vivo expanded autologous or allogeneictumor-reactive lymphocytes, e.g., dendritic cells or peptides withadjuvant; chimeric antigen receptors (CARs); cancer vaccines such asDNA-based vaccines, cytokines (e.g., IL-2), cyclophosphamide,anti-interleukin-2R immunotoxins, Prostaglandin E2 Inhibitors (e.g.,using SC-50) and/or checkpoint inhibitors including antibodies such asanti-CD137 (BMS-663513), anti-PD1 (e.g., Nivolumab,pembrolizumab/MK-3475, Pidilizumab (CT-011)), anti-PDL1 (e.g.,BMS-936559, MPDL3280A), or anti-CTLA-4 (e.g., ipilumimab; see, e.g.,Krüger et al., “Immune based therapies in cancer,” Histol Histopathol.2007 June; 22(6):687-96; Eggermont et al., “Anti-CTLA-4 antibodyadjuvant therapy in melanoma,” Semin Oncol. 2010 October; 37(5):455-9;Klinke D J 2nd, “A multiscale systems perspective on cancer,immunotherapy, and Interleukin-12,” Mol Cancer. 2010 Sep. 15; 9:242;Alexandrescu et al., “Immunotherapy for melanoma: current status andperspectives,” J Immunother. 2010 July-August; 33(6):570-90; Moschellaet al., “Combination strategies for enhancing the efficacy ofimmunotherapy in cancer patients,” Ann N Y Acad Sci. 2010 April;1194:169-78; Ganesan and Bakhshi, “Systemic therapy for melanoma,” NatlMed J India. 2010 January-February; 23(1):21-7; Golovina andVonderheide, “Regulatory T cells: overcoming suppression of T-cellimmunity,” Cancer J. 2010 July-August; 16(4):342-7. In some embodiments,the methods include administering a composition comprising tumor-pulseddendritic cells, e.g., as described in WO2009/114547 and referencescited therein. See also Shiao et al., Genes & Dev. 2011. 25: 2559-2572.

As mentioned above, adoptive cell transfer (ACT) can be used as ananti-cancer therapy. ATC can refer to the transfer of cells, mostcommonly immune-derived cells, back into the same patient or into a newrecipient host with the goal of transferring the immunologicfunctionality and characteristics into the new host. If possible, use ofautologous cells helps the recipient by minimizing graft versus hostdisease (GVHD) issues. The adoptive transfer of autologous tumorinfiltrating lymphocytes (TIL) (Besser et al., (2010) Clin. Cancer Res16 (9) 2646-55; Dudley et al., (2002) Science 298 (5594): 850-4; andDudley et al., (2005) Journal of Clinical Oncology 23 (10): 2346-57.) orgenetically re-directed peripheral blood mononuclear cells (Johnson etal., (2009) Blood 114 (3): 535-46; and Morgan et al., (2006) Science314(5796) 126-9) has been used to successfully treat patients withadvanced solid tumors, including melanoma and colorectal carcinoma, aswell as patients with CD19-expressing hematologic malignancies (Kalos etal., (2011) Science Translational Medicine 3 (95): 95ra73).

Aspects of the invention involve the adoptive transfer of immune systemcells, such as T cells, specific for selected antigens, such as tumorassociated antigens (see Maus et al., 2014, Adoptive Immunotherapy forCancer or Viruses, Annual Review of Immunology, Vol. 32: 189-225;Rosenberg and Restifo, 2015, Adoptive cell transfer as personalizedimmunotherapy for human cancer, Science Vol. 348 no. 6230 pp. 62-68;Restifo et al., 2015, Adoptive immunotherapy for cancer: harnessing theT cell response. Nat. Rev. Immunol. 12(4): 269-281; and Jenson andRiddell, 2014, Design and implementation of adoptive therapy withchimeric antigen receptor-modified T cells. Immunol Rev. 257(1):127-144). Various strategies may, for example, be employed togenetically modify T cells by altering the specificity of the T cellreceptor (TCR), for example, by introducing new TCR α and β chains withselected peptide specificity (see U.S. Pat. No. 8,697,854; PCT PatentPublications: WO2003020763, WO2004033685, WO2004044004, WO2005114215,WO2006000830, WO2008038002, WO2008039818, WO2004074322, WO2005113595,WO2006125962, WO2013166321, WO2013039889, WO2014018863, WO2014083173;U.S. Pat. No. 8,088,379).

As an alternative to, or addition to, TCR modifications, chimericantigen receptors (CARs) may be used in order to generateimmunoresponsive cells, such as T cells, specific for selected targets,such as malignant cells, with a wide variety of receptor chimeraconstructs having been described (see U.S. Pat. Nos. 5,843,728;5,851,828; 5,912,170; 6,004,811; 6,284,240; 6,392,013; 6,410,014;6,753,162; 8,211,422; and, PCT Publication WO9215322).

In general, CARs are comprised of an extracellular domain, atransmembrane domain, and an intracellular domain, wherein theextracellular domain comprises an antigen-binding domain that isspecific for a predetermined target. While the antigen-binding domain ofa CAR is often an antibody or antibody fragment (e.g., a single chainvariable fragment, scFv), the binding domain is not particularly limitedso long as it results in specific recognition of a target. For example,in some embodiments, the antigen-binding domain may comprise a receptor,such that the CAR is capable of binding to the ligand of the receptor.Alternatively, the antigen-binding domain may comprise a ligand, suchthat the CAR is capable of binding the endogenous receptor of thatligand.

The antigen-binding domain of a CAR is generally separated from thetransmembrane domain by a hinge or spacer. The spacer is also notparticularly limited, and it is designed to provide the CAR withflexibility. For example, a spacer domain may comprise a portion of ahuman Fc domain, including a portion of the CH3 domain, or the hingeregion of any immunoglobulin, such as IgA, IgD, IgE, IgG, or IgM, orvariants thereof. Furthermore, the hinge region may be modified so as toprevent off-target binding by FcRs or other potential interferingobjects. For example, the hinge may comprise an IgG4 Fc domain with orwithout a S228P, L235E, and/or N297Q mutation (according to Kabatnumbering) in order to decrease binding to FcRs. Additionalspacers/hinges include, but are not limited to, CD4, CD8, and CD28 hingeregions.

The transmembrane domain of a CAR may be derived either from a naturalor from a synthetic source. Where the source is natural, the domain maybe derived from any membrane-bound or transmembrane protein.Transmembrane regions of particular use in this disclosure may bederived from CD8, CD28, CD3, CD45, CD4, CD5, CDS, CD9, CD 16, CD22,CD33, CD37, CD64, CD80, CD86, CD 134, CD137, CD 154, TCR. Alternativelythe transmembrane domain may be synthetic, in which case it willcomprise predominantly hydrophobic residues such as leucine and valine.Preferably a triplet of phenylalanine, tryptophan and valine will befound at each end of a synthetic transmembrane domain. Optionally, ashort oligo- or polypeptide linker, preferably between 2 and 10 aminoacids in length may form the linkage between the transmembrane domainand the cytoplasmic signaling domain of the CAR. A glycine-serinedoublet provides a particularly suitable linker.

Alternative CAR constructs may be characterized as belonging tosuccessive generations. First-generation CARs typically consist of asingle-chain variable fragment of an antibody specific for an antigen,for example comprising a V_(L) linked to a V_(H) of a specific antibody,linked by a flexible linker, for example by a CD8α hinge domain and aCD8α transmembrane domain, to the transmembrane and intracellularsignaling domains of either CD3ζ or FcRγ (scFv-CD3ζ or scFv-FcRγ; seeU.S. Pat. No. 7,741,465; U.S. Pat. No. 5,912,172; U.S. Pat. No.5,906,936). Second-generation CARs incorporate the intracellular domainsof one or more costimulatory molecules, such as CD28, OX40 (CD134), or4-1BB (CD137) within the endodomain (for examplescFv-CD28/OX40/4-1BB-CD3ζ; see U.S. Pat. Nos. 8,911,993; 8,916,381;8,975,071; 9,101,584; 9,102,760; 9,102,761). Third-generation CARsinclude a combination of costimulatory endodomains, such a CD3-chain,CD97, GDI 1a-CD18, CD2, ICOS, CD27, CD2, CD7, LIGHT, LFA-1, NKG2C,B7-H3, CD30, CD40, PD-1, CD154, CDS, OX40, 4-1BB, or CD28 signalingdomains (for example scFv-CD28-4-1BB-CD3ζ or scFv-CD28-OX40-CD3ζ; seeU.S. Pat. No. 8,906,682; U.S. Pat. No. 8,399,645; U.S. Pat. No.5,686,281; PCT Publication No. WO2014134165; PCT Publication No.WO2012079000). Alternatively, costimulation may be orchestrated byexpressing CARs in antigen-specific T cells, chosen so as to beactivated and expanded following engagement of their native αβTCR, forexample by antigen on professional antigen-presenting cells, withattendant costimulation. In addition, additional engineered receptorsmay be provided on the immunoresponsive cells, for example to improvetargeting of a T-cell attack and/or minimize side effects.

Alternatively, T-cells expressing CARs may be further modified to reduceor eliminate expression of endogenous TCRs in order to reduce off-targeteffects. Reduction or elimination of endogenous TCRs can reduceoff-target effects and increase the effectiveness of the T cells (U.S.Pat. No. 9,181,527). T cells stably lacking expression of a functionalTCR may be produced using a variety of approaches. T cells internalize,sort, and degrade the entire T cell receptor as a complex, with ahalf-life of about 10 hours in resting T cells and 3 hours in stimulatedT cells (von Essen, M. et al. 2004. J. Immunol. 173:384-393). Properfunctioning of the TCR complex requires the proper stoichiometric ratioof the proteins that compose the TCR complex. TCR function also requirestwo functioning TCR zeta proteins with ITAM motifs. The activation ofthe TCR upon engagement of its MHC-peptide ligand requires theengagement of several TCRs on the same T cell, which all must signalproperly. Thus, if a TCR complex is destabilized with proteins that donot associate properly or cannot signal optimally, the T cell will notbecome activated sufficiently to begin a cellular response.

Accordingly, in some embodiments, TCR expression may be eliminated usingRNA interference (e.g., shRNA, siRNA, miRNA, etc.), CRISPR, or othermethods that target the nucleic acids encoding specific TCRs (e.g.,TCR-α and TCR-β) and/or CD3 chains in primary T cells. By blockingexpression of one or more of these proteins, the T cell will no longerproduce one or more of the key components of the TCR complex, therebydestabilizing the TCR complex and preventing cell surface expression ofa functional TCR.

In some instances, CAR may also comprise a switch mechanism forcontrolling expression and/or activation of the CAR. For example, a CARmay comprise an extracellular, transmembrane, and intracellular domain,in which the extracellular domain comprises a target-specific bindingelement that comprises a label, binding domain, or tag that is specificfor a molecule other than the target antigen that is expressed on or bya target cell. In such embodiments, the specificity of the CAR isprovided by a second construct that comprises a target antigen bindingdomain (e.g., an scFv or a bispecific antibody that is specific for boththe target antigen and the label or tag on the CAR) and a domain that isrecognized by or binds to the label, binding domain, or tag on the CAR.See, e.g., WO 2013/044225, WO 2016/000304, WO 2015/057834, WO2015/057852, WO 2016/070061, U.S. Pat. No. 9,233,125, US 2016/0129109.In this way, a T-cell that expresses the CAR can be administered to asubject, but the CAR cannot bind its target antigen until the secondcomposition comprising an antigen-specific binding domain isadministered.

Alternative switch mechanisms include CARs that require multimerizationin order to activate their signaling function (see, e.g., US2015/0368342, US 2016/0175359, US 2015/0368360) and/or an exogenoussignal, such as a small molecule drug (US 2016/0166613, Yung et al.,Science, 2015), in order to elicit a T-cell response. Some CARs may alsocomprise a “suicide switch” to induce cell death of the CAR T-cellsfollowing treatment (Buddee et al., PLoS One, 2013) or to downregulateexpression of the CAR following binding to the target antigen (WO2016/011210).

Various techniques may be used to transform target immunoresponsivecells, such as protoplast fusion, lipofection, transfection orelectroporation. A wide variety of vectors may be used, such asretroviral vectors, lentiviral vectors, adenoviral vectors,adeno-associated viral vectors, plasmids or transposons, such as aSleeping Beauty transposon (see U.S. Pat. Nos. 6,489,458; 7,148,203;7,160,682; 7,985,739; 8,227,432), may be used to introduce CARs, forexample using 2nd generation antigen-specific CARs signaling throughCD3t and either CD28 or CD137. Viral vectors may for example includevectors based on HIV, SV40, EBV, HSV or BPV.

Cells that are targeted for transformation may for example include Tcells, Natural Killer (NK) cells, cytotoxic T lymphocytes (CTL),regulatory T cells, human embryonic stem cells, tumor-infiltratinglymphocytes (TIL) or a pluripotent stem cell from which lymphoid cellsmay be differentiated. T cells expressing a desired CAR may for examplebe selected through co-culture with γ-irradiated activating andpropagating cells (AaPC), which co-express the cancer antigen andco-stimulatory molecules. The engineered CAR T-cells may be expanded,for example by co-culture on AaPC in presence of soluble factors, suchas IL-2 and IL-21. This expansion may for example be carried out so asto provide memory CAR+ T cells (which may for example be assayed bynon-enzymatic digital array and/or multi-panel flow cytometry). In thisway, CAR T cells may be provided that have specific cytotoxic activityagainst antigen-bearing tumors (optionally in conjunction withproduction of desired chemokines such as interferon-γ). CAR T cells ofthis kind may for example be used in animal models, for example to treattumor xenografts.

Approaches such as the foregoing may be adapted to provide methods oftreating and/or increasing survival of a subject having a disease, suchas a neoplasia, for example by administering an effective amount of animmunoresponsive cell comprising an antigen recognizing receptor thatbinds a selected antigen, wherein the binding activates theimmunoreponsive cell, thereby treating or preventing the disease (suchas a neoplasia, a pathogen infection, an autoimmune disorder, or anallogeneic transplant reaction).

In some embodiments, the treatment can be administrated into patientsundergoing an immunosuppressive treatment. The cells, or population ofcells, may be made resistant to at least one immunosuppressive agent dueto the inactivation of a gene encoding a receptor for suchimmunosuppressive agent. Not being bound by a theory, theimmunosuppressive treatment should help the selection and expansion ofthe immunoresponsive or T cells according to the invention within thepatient.

The administration of the cells or population of cells according to thepresent invention may be carried out in any convenient manner, includingby aerosol inhalation, injection, ingestion, transfusion, implantationor transplantation. The cells or population of cells may be administeredto a patient subcutaneously, intradermally, intratumorally,intranodally, intramedullary, intramuscularly, intrathecally, byintravenous or intralymphatic injection, or intraperitoneally. In someembodiments, the disclosed CARs may be delivered or administered into acavity formed by the resection of tumor tissue (i.e. intracavitydelivery) or directly into a tumor prior to resection (i.e. intratumoraldelivery). In one embodiment, the cell compositions of the presentinvention are preferably administered by intravenous injection.

The administration of the cells or population of cells can consist ofthe administration of 10⁴-10⁹ cells per kg body weight, preferably 10⁵to 10⁶ cells/kg body weight including all integer values of cell numberswithin those ranges. Dosing in CAR T cell therapies may for exampleinvolve administration of from 10⁶ to 10⁹ cells/kg, with or without acourse of lymphodepletion, for example with cyclophosphamide. The cellsor population of cells can be administrated in one or more doses. Inanother embodiment, the effective amount of cells are administrated as asingle dose. In another embodiment, the effective amount of cells areadministrated as more than one dose over a period time. Timing ofadministration is within the judgment of managing physician and dependson the clinical condition of the patient. The cells or population ofcells may be obtained from any source, such as a blood bank or a donor.While individual needs vary, determination of optimal ranges ofeffective amounts of a given cell type for a particular disease orconditions are within the skill of one in the art. An effective amountmeans an amount which provides a therapeutic or prophylactic benefit.The dosage administrated will be dependent upon the age, health andweight of the recipient, kind of concurrent treatment, if any, frequencyof treatment and the nature of the effect desired.

In another embodiment, the effective amount of cells or compositioncomprising those cells are administrated parenterally. Theadministration can be an intravenous administration. The administrationcan be directly done by injection within a tumor.

To guard against possible adverse reactions, engineered immunoresponsivecells may be equipped with a transgenic safety switch, in the form of atransgene that renders the cells vulnerable to exposure to a specificsignal. For example, the herpes simplex viral thymidine kinase (TK) genemay be used in this way, for example by introduction into allogeneic Tlymphocytes used as donor lymphocyte infusions following stem celltransplantation (Greco, et al., Improving the safety of cell therapywith the TK-suicide gene. Front. Pharmacol. 2015; 6: 95). In such cells,administration of a nucleoside prodrug such as ganciclovir or acyclovircauses cell death. Alternative safety switch constructs includeinducible caspase 9, for example triggered by administration of asmall-molecule dimerizer that brings together two nonfunctional icasp9molecules to form the active enzyme. A wide variety of alternativeapproaches to implementing cellular proliferation controls have beendescribed (see U.S. Patent Publication No. 20130071414; PCT PatentPublication WO2011146862; PCT Patent Publication WO2014011987; PCTPatent Publication WO2013040371; Zhou et al. BLOOD, 2014,123/25:3895-3905; Di Stasi et al., The New England Journal of Medicine2011; 365:1673-1683; Sadelain M, The New England Journal of Medicine2011; 365:1735-173; Ramos et al., Stem Cells 28(6):1107-15 (2010)).

In a further refinement of adoptive therapies, genome editing may beused to tailor immunoresponsive cells to alternative implementations,for example providing edited CAR T cells (see Poirot et al., 2015,Multiplex genome edited T-cell manufacturing platform for“off-the-shelf” adoptive T-cell immunotherapies, Cancer Res 75 (18):3853). For example, the CAR T cells can comprise a T cell with CD5Land/or p40 knockouts. Cells may be edited using any CRISPR system andmethod of use thereof as described herein. CRISPR systems may bedelivered to an immune cell by any method described herein. In preferredembodiments, cells are edited ex vivo and transferred to a subject inneed thereof. Immunoresponsive cells, CAR T cells or any cells used foradoptive cell transfer may be edited. Editing may be performed toeliminate potential alloreactive T-cell receptors (TCR), disrupt thetarget of a chemotherapeutic agent, block an immune checkpoint, activatea T cell, and/or increase the differentiation and/or proliferation offunctionally exhausted or dysfunctional CD8+ T-cells (see PCT PatentPublications: WO2013176915, WO2014059173, WO2014172606, WO2014184744,and WO2014191128). Editing may result in inactivation of a gene.

By inactivating a gene it is intended that the gene of interest is notexpressed in a functional protein form. In a particular embodiment, theCRISPR system specifically catalyzes cleavage in one targeted genethereby inactivating said targeted gene. The nucleic acid strand breakscaused are commonly repaired through the distinct mechanisms ofhomologous recombination or non-homologous end joining (NHEJ). However,NHEJ is an imperfect repair process that often results in changes to theDNA sequence at the site of the cleavage. Repair via non-homologous endjoining (NHEJ) often results in small insertions or deletions (Indel)and can be used for the creation of specific gene knockouts. Cells inwhich a cleavage induced mutagenesis event has occurred can beidentified and/or selected by well-known methods in the art.

T cell receptors (TCR) are cell surface receptors that participate inthe activation of T cells in response to the presentation of antigen.The TCR is generally made from two chains, α and β, which assemble toform a heterodimer and associates with the CD3-transducing subunits toform the T cell receptor complex present on the cell surface. Each α andβ chain of the TCR consists of an immunoglobulin-like N-terminalvariable (V) and constant (C) region, a hydrophobic transmembranedomain, and a short cytoplasmic region. As for immunoglobulin molecules,the variable region of the α and β chains are generated by V(D)Jrecombination, creating a large diversity of antigen specificitieswithin the population of T cells. However, in contrast toimmunoglobulins that recognize intact antigen, T cells are activated byprocessed peptide fragments in association with an MHC molecule,introducing an extra dimension to antigen recognition by T cells, knownas MHC restriction. Recognition of MHC disparities between the donor andrecipient through the T cell receptor leads to T cell proliferation andthe potential development of GVHD. The inactivation of TCRα or TCRβ canresult in the elimination of the TCR from the surface of T cellspreventing recognition of alloantigen and thus GVHD. However, TCRdisruption generally results in the elimination of the CD3 signalingcomponent and alters the means of further T cell expansion.

Allogeneic cells are rapidly rejected by the host immune system. It hasbeen demonstrated that, allogeneic leukocytes present in non-irradiatedblood products will persist for no more than 5 to 6 days (Boni, Muranskiet al. 2008 Blood 1; 112(12):4746-54). Thus, to prevent rejection ofallogeneic cells, the host's immune system usually has to be suppressedto some extent. However, in the case of adoptive cell transfer the useof immunosuppressive drugs also have a detrimental effect on theintroduced therapeutic T cells. Therefore, to effectively use anadoptive immunotherapy approach in these conditions, the introducedcells would need to be resistant to the immunosuppressive treatment.Thus, in a particular embodiment, the present invention furthercomprises a step of modifying T cells to make them resistant to animmunosuppressive agent, preferably by inactivating at least one geneencoding a target for an immunosuppressive agent. An immunosuppressiveagent is an agent that suppresses immune function by one of severalmechanisms of action. An immunosuppressive agent can be, but is notlimited to a calcineurin inhibitor, a target of rapamycin, aninterleukin-2 receptor α-chain blocker, an inhibitor of inosinemonophosphate dehydrogenase, an inhibitor of dihydrofolic acidreductase, a corticosteroid or an immunosuppressive antimetabolite. Thepresent invention allows conferring immunosuppressive resistance to Tcells for immunotherapy by inactivating the target of theimmunosuppressive agent in T cells. As non-limiting examples, targetsfor an immunosuppressive agent can be a receptor for animmunosuppressive agent such as: CD52, glucocorticoid receptor (GR), aFKBP family gene member and a cyclophilin family gene member.

Immune checkpoints are inhibitory pathways that slow down or stop immunereactions and prevent excessive tissue damage from uncontrolled activityof immune cells. In certain embodiments, the immune checkpoint targetedis the programmed death-1 (PD-1 or CD279) gene (PDCD1). In otherembodiments, the immune checkpoint targeted is cytotoxicT-lymphocyte-associated antigen (CTLA-4). In additional embodiments, theimmune checkpoint targeted is another member of the CD28 and CTLA4 Igsuperfamily such as BTLA, LAG3, ICOS, PDL1 or KIR. In further additionalembodiments, the immune checkpoint targeted is a member of the TNFRsuperfamily such as CD40, OX40, CD137, GITR, CD27 or TIM-3.

Additional immune checkpoints include Src homology 2 domain-containingprotein tyrosine phosphatase 1 (SHP-1) (Watson H A, et al., SHP-1: thenext checkpoint target for cancer immunotherapy? Biochem Soc Trans. 2016Apr. 15; 44(2):356-62). SHP-1 is a widely expressed inhibitory proteintyrosine phosphatase (PTP). In T-cells, it is a negative regulator ofantigen-dependent activation and proliferation. It is a cytosolicprotein, and therefore not amenable to antibody-mediated therapies, butits role in activation and proliferation makes it an attractive targetfor genetic manipulation in adoptive transfer strategies, such aschimeric antigen receptor (CAR) T cells. Immune checkpoints may alsoinclude T cell immunoreceptor with Ig and ITIM domains(TIGIT/Vstm3/WUCAM/VSIG9) and VISTA (Le Mercier I, et al., (2015) BeyondCTLA-4 and PD-1, the generation Z of negative checkpoint regulators.Front. Immunol. 6:418).

WO2014172606 relates to the use of MT1 and/or MT1 inhibitors to increaseproliferation and/or activity of exhausted CD8+ T-cells and to decreaseCD8+ T-cell exhaustion (e.g., decrease functionally exhausted orunresponsive CD8+ immune cells). In certain embodiments,metallothioneins are targeted by gene editing in adoptively transferredT cells.

In certain embodiments, targets of gene editing may be at least onetargeted locus involved in the expression of an immune checkpointprotein. Such targets may include, but are not limited to CTLA4, PPP2CA,PPP2CB, PTPN6, PTPN22, PDCD1, ICOS (CD278), PDL1, KIR, LAG3, HAVCR2,BTLA, CD160, TIGIT, CD96, CRTAM, LAIR1, SIGLEC7, SIGLEC9, CD244 (2B4),TNFRSF10B, TNFRSF10A, CASP8, CASP10, CASP3, CASP6, CASP7, FADD, FAS,TGFBRII, TGFRBRI, SMAD2, SMAD3, SMAD4, SMAD10, SKI, SKIL, TGIF1, IL10RA,IL10RB, HMOX2, IL6R, IL6ST, EIF2AK4, CSK, PAG1, SIT1, FOXP3, PRDM1,BATF, VISTA, GUCY1A2, GUCY1A3, GUCY1B2, GUCY1B3, MT1, MT2, CD40, OX40,CD137, GITR, CD27, SHP-1, T-BET, RORC, or TIM-3. In preferredembodiments, the gene locus involved in the expression of PD-1 or CTLA-4genes is targeted. In other preferred embodiments, combinations of genesare targeted, such as but not limited to PD-1 and TIGIT. In preferredembodiments, the novel genes or gene combinations described herein aretargeted or modulated.

In other embodiments, at least two genes are edited. Pairs of genes mayinclude, but are not limited to PD1 and TCRα, PD1 and TCRβ, CTLA-4 andTCRα, CTLA-4 and TCRβ, LAG3 and TCRα, LAG3 and TCRβ, Tim3 and TCRα, Tim3and TCRβ, BTLA and TCRα, BTLA and TCRβ, BY55 and TCRα, BY55 and TCRβ,TIGIT and TCRα, TIGIT and TCRβ, B7H5 and TCRα, B7H5 and TCRβ, LAIR1 andTCRα, LAIR1 and TCRβ, SIGLEC10 and TCRα, SIGLEC10 and TCRβ, 2B4 andTCRα, 2B4 and TCRβ.

Whether prior to or after genetic modification of the T cells, the Tcells can be activated and expanded generally using methods asdescribed, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055;6,905,680; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,232,566;7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and 7,572,631. Tcells can be expanded in vitro or in vivo.

Immune cells may be obtained using any method known in the art. In oneembodiment T cells that have infiltrated a tumor are isolated. T cellsmay be removed during surgery. T cells may be isolated after removal oftumor tissue by biopsy. T cells may be isolated by any means known inthe art. In one embodiment the method may comprise obtaining a bulkpopulation of T cells from a tumor sample by any suitable method knownin the art. For example, a bulk population of T cells can be obtainedfrom a tumor sample by dissociating the tumor sample into a cellsuspension from which specific cell populations can be selected.Suitable methods of obtaining a bulk population of T cells may include,but are not limited to, any one or more of mechanically dissociating(e.g., mincing) the tumor, enzymatically dissociating (e.g., digesting)the tumor, and aspiration (e.g., as with a needle).

The bulk population of T cells obtained from a tumor sample may compriseany suitable type of T cell. Preferably, the bulk population of T cellsobtained from a tumor sample comprises tumor infiltrating lymphocytes(TILs).

The tumor sample may be obtained from any mammal. Unless statedotherwise, as used herein, the term “mammal” refers to any mammalincluding, but not limited to, mammals of the order Logomorpha, such asrabbits; the order Carnivora, including Felines (cats) and Canines(dogs); the order Artiodactyla, including Bovines (cows) and Swines(pigs); or of the order Perssodactyla, including Equines (horses). Themammals may be non-human primates, e.g., of the order Primates, Ceboids,or Simoids (monkeys) or of the order Anthropoids (humans and apes). Insome embodiments, the mammal may be a mammal of the order Rodentia, suchas mice and hamsters. Preferably, the mammal is a non-human primate or ahuman. An especially preferred mammal is the human.

T cells can be obtained from a number of sources, including peripheralblood mononuclear cells, bone marrow, lymph node tissue, spleen tissue,and tumors. In certain embodiments of the present invention, T cells canbe obtained from a unit of blood collected from a subject using anynumber of techniques known to the skilled artisan, such as Ficollseparation. In one preferred embodiment, cells from the circulatingblood of an individual are obtained by apheresis or leukapheresis. Theapheresis product typically contains lymphocytes, including T cells,monocytes, granulocytes, B cells, other nucleated white blood cells, redblood cells, and platelets. In one embodiment, the cells collected byapheresis may be washed to remove the plasma fraction and to place thecells in an appropriate buffer or media for subsequent processing steps.In one embodiment of the invention, the cells are washed with phosphatebuffered saline (PBS). In an alternative embodiment, the wash solutionlacks calcium and may lack magnesium or may lack many if not alldivalent cations. Initial activation steps in the absence of calciumlead to magnified activation. As those of ordinary skill in the artwould readily appreciate a washing step may be accomplished by methodsknown to those in the art, such as by using a semi-automated“flow-through” centrifuge (for example, the Cobe 2991 cell processor)according to the manufacturer's instructions. After washing, the cellsmay be resuspended in a variety of biocompatible buffers, such as, forexample, Ca-free, Mg-free PBS. Alternatively, the undesirable componentsof the apheresis sample may be removed and the cells directlyresuspended in culture media.

In another embodiment, T cells are isolated from peripheral bloodlymphocytes by lysing the red blood cells and depleting the monocytes,for example, by centrifugation through a PERCOLL™ gradient. A specificsubpopulation of cells, such as CD28+, CD4+, CDC, CD45RA+, and CD45RO+ Tcells, can be further isolated by positive or negative selectiontechniques. For example, in one preferred embodiment, T cells areisolated by incubation with anti-CD3/anti-CD28 (i.e., 3×28)-conjugatedbeads, such as DYNABEADS® M-450 CD3/CD28 T, or XCYTE DYNABEADS™ for atime period sufficient for positive selection of the desired T cells. Inone embodiment, the time period is about 30 minutes. In a furtherembodiment, the time period ranges from 30 minutes to 36 hours or longerand all integer values there between. In a further embodiment, the timeperiod is at least 1, 2, 3, 4, 5, or 6 hours. In yet another preferredembodiment, the time period is 10 to 24 hours. In one preferredembodiment, the incubation time period is 24 hours. For isolation of Tcells from patients with leukemia, use of longer incubation times, suchas 24 hours, can increase cell yield. Longer incubation times may beused to isolate T cells in any situation where there are few T3 cells ascompared to other cell types, such in isolating tumor infiltratinglymphocytes (TIL) from tumor tissue or from immunocompromisedindividuals. Further, use of longer incubation times can increase theefficiency of capture of CD8+ T cells.

Enrichment of a T cell population by negative selection can beaccomplished with a combination of antibodies directed to surfacemarkers unique to the negatively selected cells. A preferred method iscell sorting and/or selection via negative magnetic immunoadherence orflow cytometry that uses a cocktail of monoclonal antibodies directed tocell surface markers present on the cells negatively selected. Forexample, to enrich for CD4+ cells by negative selection, a monoclonalantibody cocktail typically includes antibodies to CD14, CD20, CD11b,CD16, HLA-DR, and CD8.

Further, monocyte populations (i.e., CD14+ cells) may be depleted fromblood preparations by a variety of methodologies, including anti-CD14coated beads or columns, or utilization of the phagocytotic activity ofthese cells to facilitate removal. Accordingly, in one embodiment, theinvention uses paramagnetic particles of a size sufficient to beengulfed by phagocytotic monocytes. In certain embodiments, theparamagnetic particles are commercially available beads, for example,those produced by Life Technologies under the trade name Dynabeads™. Inone embodiment, other non-specific cells are removed by coating theparamagnetic particles with “irrelevant” proteins (e.g., serum proteinsor antibodies). Irrelevant proteins and antibodies include thoseproteins and antibodies or fragments thereof that do not specificallytarget the T cells to be isolated. In certain embodiments the irrelevantbeads include beads coated with sheep anti-mouse antibodies, goatanti-mouse antibodies, and human serum albumin.

In brief, such depletion of monocytes is performed by preincubating Tcells isolated from whole blood, apheresed peripheral blood, or tumorswith one or more varieties of irrelevant or non-antibody coupledparamagnetic particles at any amount that allows for removal ofmonocytes (approximately a 20:1 bead:cell ratio) for about 30 minutes to2 hours at 22 to 37 degrees C., followed by magnetic removal of cellswhich have attached to or engulfed the paramagnetic particles. Suchseparation can be performed using standard methods available in the art.For example, any magnetic separation methodology may be used including avariety of which are commercially available, (e.g., DYNAL® MagneticParticle Concentrator (DYNAL MPC®)). Assurance of requisite depletioncan be monitored by a variety of methodologies known to those ofordinary skill in the art, including flow cytometric analysis of CD14positive cells, before and after depletion.

For isolation of a desired population of cells by positive or negativeselection, the concentration of cells and surface (e.g., particles suchas beads) can be varied. In certain embodiments, it may be desirable tosignificantly decrease the volume in which beads and cells are mixedtogether (i.e., increase the concentration of cells), to ensure maximumcontact of cells and beads. For example, in one embodiment, aconcentration of 2 billion cells/ml is used. In one embodiment, aconcentration of 1 billion cells/ml is used. In a further embodiment,greater than 100 million cells/ml is used. In a further embodiment, aconcentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 millioncells/ml is used. In yet another embodiment, a concentration of cellsfrom 75, 80, 85, 90, 95, or 100 million cells/ml is used. In furtherembodiments, concentrations of 125 or 150 million cells/ml can be used.Using high concentrations can result in increased cell yield, cellactivation, and cell expansion. Further, use of high cell concentrationsallows more efficient capture of cells that may weakly express targetantigens of interest, such as CD28-negative T cells, or from sampleswhere there are many tumor cells present (i.e., leukemic blood, tumortissue, etc). Such populations of cells may have therapeutic value andwould be desirable to obtain. For example, using high concentration ofcells allows more efficient selection of CD8+ T cells that normally haveweaker CD28 expression.

In a related embodiment, it may be desirable to use lower concentrationsof cells. By significantly diluting the mixture of T cells and surface(e.g., particles such as beads), interactions between the particles andcells is minimized. This selects for cells that express high amounts ofdesired antigens to be bound to the particles. For example, CD4+ T cellsexpress higher levels of CD28 and are more efficiently captured thanCD8+ T cells in dilute concentrations. In one embodiment, theconcentration of cells used is 5×10⁶/ml. In other embodiments, theconcentration used can be from about 1×10⁵/ml to 1×10⁶/ml, and anyinteger value in between.

T cells can also be frozen. Wishing not to be bound by theory, thefreeze and subsequent thaw step provides a more uniform product byremoving granulocytes and to some extent monocytes in the cellpopulation. After a washing step to remove plasma and platelets, thecells may be suspended in a freezing solution. While many freezingsolutions and parameters are known in the art and will be useful in thiscontext, one method involves using PBS containing 20% DMSO and 8% humanserum albumin, or other suitable cell freezing media, the cells then arefrozen to −80° C. at a rate of 1° per minute and stored in the vaporphase of a liquid nitrogen storage tank. Other methods of controlledfreezing may be used as well as uncontrolled freezing immediately at−20° C. or in liquid nitrogen.

T cells for use in the present invention may also be antigen-specific Tcells. For example, tumor-specific T cells can be used. In certainembodiments, antigen-specific T cells can be isolated from a patient ofinterest, such as a patient afflicted with a cancer or an infectiousdisease. In one embodiment neoepitopes are determined for a subject andT cells specific to these antigens are isolated. Antigen-specific cellsfor use in expansion may also be generated in vitro using any number ofmethods known in the art, for example, as described in U.S. PatentPublication No. US 20040224402 entitled, Generation And Isolation ofAntigen-Specific T Cells, or in U.S. Pat. No. 6,040,177.Antigen-specific cells for use in the present invention may also begenerated using any number of methods known in the art, for example, asdescribed in Current Protocols in Immunology, or Current Protocols inCell Biology, both published by John Wiley & Sons, Inc., Boston, Mass.

In a related embodiment, it may be desirable to sort or otherwisepositively select (e.g. via magnetic selection) the antigen specificcells prior to or following one or two rounds of expansion. Sorting orpositively selecting antigen-specific cells can be carried out usingpeptide-MHC tetramers (Altman, et al., Science. 1996 Oct. 4;274(5284):94-6). In another embodiment the adaptable tetramer technologyapproach is used (Andersen et al., 2012 Nat Protoc. 7:891-902).Tetramers are limited by the need to utilize predicted binding peptidesbased on prior hypotheses, and the restriction to specific HLAs.Peptide-MHC tetramers can be generated using techniques known in the artand can be made with any MHC molecule of interest and any antigen ofinterest as described herein. Specific epitopes to be used in thiscontext can be identified using numerous assays known in the art. Forexample, the ability of a polypeptide to bind to MHC class I may beevaluated indirectly by monitoring the ability to promote incorporationof ¹²⁵I labeled β2-microglobulin (β2m) into MHC class I/β2m/peptideheterotrimeric complexes (see Parker et al., J. Immunol. 152:163, 1994).

In one embodiment cells are directly labeled with an epitope-specificreagent for isolation by flow cytometry followed by characterization ofphenotype and TCRs. In one T cells are isolated by contacting the T cellspecific antibodies. Sorting of antigen-specific T cells, or generallyany cells of the present invention, can be carried out using any of avariety of commercially available cell sorters, including, but notlimited to, MoFlo sorter (DakoCytomation, Fort Collins, Colo.),FACSAria™, FACSArray™, FACSVantage™, BD™ LSR II, and FACSCalibur™ (BDBiosciences, San Jose, Calif.).

In a preferred embodiment, the method comprises selecting cells thatalso express CD3, The method may comprise specifically selecting thecells in any suitable manner. Preferably, the selecting is carried outusing flow cytometry. The flow cytometry may be carried out using anysuitable method known in the art. The flow cytometry may employ anysuitable antibodies and stains. Preferably, the antibody is chosen suchthat it specifically recognizes and binds to the particular biomarkerbeing selected. For example, the specific selection of CD3, CD8, TIM-3,LAG-3, 4-1BB, or PD-1 may be carried out using anti-CD3, anti-CD8,anti-TIM-3, anti-LAG-3, anti-4-113B, or anti-PD-1 antibodies,respectively. The antibody or antibodies may be conjugated to a bead(e.g., a magnetic bead) or to a fluorochrome. Preferably, the flowcytometry is fluorescence-activated cell sorting (FACS). TCRs expressedon T cells can be selected based on reactivity to autologous tumors.Additionally, T cells that are reactive to tumors can be selected forbased on markers using the methods described in patent publication Nos.WO2014133567 and WO2014133568, herein incorporated by reference in theirentirety. Additionally, activated T cells can be selected for based onsurface expression of CD107a.

In one embodiment of the invention, the method further comprisesexpanding the numbers of T cells in the enriched cell population. Suchmethods are described in U.S. Pat. No. 8,637,307 and is hereinincorporated by reference in its entirety. The numbers of T cells may beincreased at least about 3-fold (or 4-, 5-, 6-, 7-, 8-, or 9-fold), morepreferably at least about 10-fold (or 20-, 30-, 40-, 50-, 60-, 70-, 80-,or 90-fold), more preferably at least about 100-fold, more preferably atleast about 1,000 fold, or most preferably at least about 100,000-fold.The numbers of T cells may be expanded using any suitable method knownin the art. Exemplary methods of expanding the numbers of cells aredescribed in patent publication No. WO 2003057171, U.S. Pat. No.8,034,334, and U.S. Patent Application Publication No. 2012/0244133,each of which is incorporated herein by reference.

In one embodiment, ex vivo T cell expansion can be performed byisolation of T cells and subsequent stimulation or activation followedby further expansion. In one embodiment of the invention, the T cellsmay be stimulated or activated by a single agent. In another embodiment,T cells are stimulated or activated with two agents, one that induces aprimary signal and a second that is a co-stimulatory signal. Ligandsuseful for stimulating a single signal or stimulating a primary signaland an accessory molecule that stimulates a second signal may be used insoluble form. Ligands may be attached to the surface of a cell, to anEngineered Multivalent Signaling Platform (EMSP), or immobilized on asurface. In a preferred embodiment both primary and secondary agents areco-immobilized on a surface, for example a bead or a cell. In oneembodiment, the molecule providing the primary activation signal may bea CD3 ligand, and the co-stimulatory molecule may be a CD28 ligand or4-1BB ligand.

Antibodies to CD5L, CD5L: CD5L, or CD5L:p40 Heterodimer

As already mentioned, some embodiments comprise methods that includeadministering an antibody or an antigen fragment thereof that binds toand inhibits the activity of CD5L monomer, CD5L homodimer, or theCD5L:p40 heterodimer, e.g., that specifically inhibits binding of theCD5L monomer, CD5L homodimer, or CD5L:p40 heterodimer to the IL-23receptor, or that specifically inhibits formation of the CD5L homodimeror CD5L:p40 heterodimer.

The term “antibody” as used herein refers to an immunoglobulin moleculeor an antigen-binding portion thereof. Examples of antigen-bindingportions of immunoglobulin molecules include F(ab) and F(ab′)2fragments, which retain the ability to bind antigen. The antibody can bepolyclonal, monoclonal, recombinant, chimeric, de-immunized orhumanized, fully human, non-human, (e.g., murine), or single chainantibody. In some embodiments the antibody has effector function and canfix complement. In some embodiments, the antibody has reduced or noability to bind an Fc receptor. For example, the antibody can be anisotype or subtype, fragment or other mutant, which does not supportbinding to an Fc receptor, e.g., it has a mutagenized or deleted Fcreceptor binding region. Methods for making antibodies and fragmentsthereof are known in the art, see, e.g., Harlow et. al., editors,Antibodies: A Laboratory Manual (1988); Goding, Monoclonal Antibodies:Principles and Practice, (N.Y. Academic Press 1983); Howard and Kaser,Making and Using Antibodies: A Practical Handbook (CRC Press; 1stedition, Dec. 13, 2006); Kontermann and Dühel, Antibody EngineeringVolume 1 (Springer Protocols) (Springer; 2nd ed., May 21, 2010); Lo,Antibody Engineering: Methods and Protocols (Methods in MolecularBiology) (Humana Press; Nov. 10, 2010); and Dübel, Handbook ofTherapeutic Antibodies: Technologies, Emerging Developments and ApprovedTherapeutics, (Wiley-VCH; 1 edition Sep. 7, 2010).

Inhibitory Nucleic Acids

Some embodiments comprise decreasing protein expression (e.g., CD5L orp40 expression) with inhibitory nucleic acids. Inhibitory nucleic acidsuseful in the present methods and compositions include antisenseoligonucleotides, ribozymes, external guide sequence (EGS)oligonucleotides, siRNA compounds, single- or double-stranded RNAinterference (RNAi) compounds such as siRNA compounds, modifiedbases/locked nucleic acids (LNAs), antagomirs, peptide nucleic acids(PNAs), ribozymes, and other oligomeric compounds or oligonucleotidemimetics which hybridize to at least a portion of the target nucleicacid and modulate its function. In some embodiments, the inhibitorynucleic acids include antisense RNA, antisense DNA, chimeric antisenseoligonucleotides, antisense oligonucleotides comprising modifiedlinkages, interference RNA (RNAi), short interfering RNA (siRNA); amicro, interfering RNA (miRNA); a small, temporal RNA (stRNA); or ashort, hairpin RNA (shRNA); small RNA-induced gene activation (RNAa);small activating RNAs (saRNAs), or combinations thereof. See, e.g., WO2010040112; Burnett and Rossi (2012) Chem Biol. 19 (1):60-71; andWO2015130968, which is incorporated herein by reference in its entirety.

In some embodiments, the inhibitory nucleic acids are 10 to 50, 13 to50, or 13 to 30 nucleotides in length. One having ordinary skill in theart will appreciate that this embodies oligonucleotides having antisenseportions of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length, or any rangethere within. In some embodiments, the oligonucleotides are 15nucleotides in length. In some embodiments, the antisense oroligonucleotide compounds of the invention are 12 or 13 to 30nucleotides in length. One having ordinary skill in the art willappreciate that this embodies inhibitory nucleic acids having antisenseportions of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29 or 30 nucleotides in length, or any range there within.

In some embodiments, the inhibitory nucleic acids are chimericoligonucleotides that contain two or more chemically distinct regions,each made up of at least one nucleotide. These oligonucleotidestypically contain at least one region of modified nucleotides thatconfers one or more beneficial properties (such as, for example,increased nuclease resistance, increased uptake into cells, increasedbinding affinity for the target) and a region that is a substrate forenzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. Chimericinhibitory nucleic acids of the invention may be formed as compositestructures of two or more oligonucleotides, modified oligonucleotides,oligonucleosides and/or oligonucleotide mimetics as described above.Such compounds have also been referred to in the art as hybrids orgapmers. Representative United States patents that teach the preparationof such hybrid structures comprise, but are not limited to, U.S. Pat.Nos. 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711;5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; 5,700,922;8,604,192; 8,697,663; 8,703,728; 8,796,437; 8,865,677; and 8,883,752each of which is herein incorporated by reference.

In some embodiments, the inhibitory nucleic acid comprises at least onenucleotide modified at the 2′ position of the sugar, most preferably a2′-O-alkyl, 2′-O-alkyl-O-alkyl or 2′-fluoro-modified nucleotide. Inother preferred embodiments, RNA modifications include 2′-fluoro,2′-amino and 2′ O-methyl modifications on the ribose of pyrimidines,abasic residues or an inverted base at the 3′ end of the RNA. Suchmodifications are routinely incorporated into oligonucleotides and theseoligonucleotides have been shown to have a higher Tm (i.e., highertarget binding affinity) than; 2′-deoxyoligonucleotides against a giventarget.

A number of nucleotide and nucleoside modifications have been shown tomake the oligonucleotide into which they are incorporated more resistantto nuclease digestion than the native oligodeoxynucleotide; thesemodified oligos survive intact for a longer time than unmodifiedoligonucleotides. Specific examples of modified oligonucleotides includethose comprising modified backbones, for example, phosphorothioates,phosphotriesters, methyl phosphonates, short chain alkyl or cycloalkylintersugar linkages or short chain heteroatomic or heterocyclicintersugar linkages. Most preferred are oligonucleotides withphosphorothioate backbones and those with heteroatom backbones,particularly CH2-NH—O—CH2, CH, ˜N(CH3)˜O˜CH2 (known as amethylene(methylimino) or MMI backbone], CH2-O—N(CH3)-CH2, CH2-N(CH3)-N(CH3)-CH2 and O—N(CH3)-CH2-CH2 backbones, wherein the nativephosphodiester backbone is represented as O—P—O—CH); amide backbones (DeMesmaeker (1995) Ace. Chem. Res. 28:366-374); morpholino backbonestructures (Summerton and Weller, U.S. Pat. No. 5,034,506); peptidenucleic acid (PNA) backbone (wherein the phosphodiester backbone of theoligonucleotide is replaced with a polyamide backbone, the nucleotidesbeing bound directly or indirectly to the aza nitrogen atoms of thepolyamide backbone, Nielsen (1991) Science 254, 1497).Phosphorus-containing linkages include, but are not limited to,phosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkylphosphotriesters, methyl and other alkylphosphonates comprising 3′alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates comprising 3′-amino phosphoramidate andaminoalkylphosphoramidates, phosphonoacetate phosphoramidates,thionophosphoramidates, thionoalkylphosphonates,thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′linkages, 2′-5′ linked analogs of these, and those having invertedpolarity wherein the adjacent pairs of nucleoside units are linked 3′-5′to 5′-3′ or 2′-5′ to 5′-2′; see U.S. Pat. Nos. 3,687,808; 4,469,863;4,476,301; 5,023,243; 5, 177,196; 5,188,897; 5,264,423; 5,276,019;5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111;5,563, 253; 5,571,799; 5,587,361; and 5,625,050.

Morpholino-based oligomeric compounds are described in Dwaine A. Braaschand David R. Corey (2002) Biochemistry 41(14), 4503-4510); Genesis,volume 30, issue 3, 2001; Heasman, (2002) Dev. Biol. 243, 209-214;Nasevicius (2000) Nat. Genet. 26, 216-220; Lacerra (2000) Proc. Natl.Acad. Sci. 97, 9591-9596; and U.S. Pat. No. 5,034,506, issued Jul. 23,1991. Cyclohexenyl nucleic acid oligonucleotide mimetics are describedin Wang (2000) Am. Chem. Soc. 122, 8595-8602.

Modified oligonucleotide backbones that do not include a phosphorus atomtherein have backbones that are formed by short chain alkyl orcycloalkyl internucleoside linkages, mixed heteroatom and alkyl orcycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These comprisethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH2 component parts; see U.S. Pat. Nos. 5,034,506; 5,166,315;5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264, 562; 5, 264,564;5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307;5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046;5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437;5,677,439; and 8,927,513 each of which is herein incorporated byreference.

One or more substituted sugar moieties can also be included, e.g., oneof the following at the 2′ position: OH, SH, SCH₃, F, OCN, OCH₃, OCH₃O(CH₂)n CH₃, O(CH₂)n NH₂ or O(CH₂)n CH₃ where n is from 1 to about 10;Ci to C10 lower alkyl, alkoxyalkoxy, substituted lower alkyl, alkaryl oraralkyl; Cl; Br; CN; CF3; OCF3; O-, S-, or N-alkyl; O-, S-, orN-alkenyl; SOCH3; SO2 CH3; ONO2; NO2; N3; NH2; heterocycloalkyl;heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl;an RNA cleaving group; a reporter group; an intercalator; a group forimproving the pharmacokinetic properties of an oligonucleotide; or agroup for improving the pharmacodynamic properties of an oligonucleotideand other substituents having similar properties. A preferredmodification includes 2′-methoxyethoxy [2′-0-CH₂CH₂OCH₃, also known as2′-O-(2-methoxyethyl)] (Martin (1995) Helv. Chim. Acta 78, 486). Otherpreferred modifications include 2′-methoxy (2′-0-CH₃), 2′-propoxy(2′-OCH₂ CH₂CH₃) and 2′-fluoro (2′-F). Similar modifications may also bemade at other positions on the oligonucleotide, particularly the 3′position of the sugar on the 3′ terminal nucleotide and the 5′ positionof 5′ terminal nucleotide. Oligonucleotides may also have sugar mimeticssuch as cyclobutyls in place of the pentofuranosyl group.

Inhibitory nucleic acids can also include, additionally oralternatively, nucleobase (often referred to in the art simply as“base”) modifications or substitutions. As used herein, “unmodified” or“natural” nucleobases include adenine (A), guanine (G), thymine (T),cytosine (C) and uracil (U). Modified nucleobases include nucleobasesfound only infrequently or transiently in natural nucleic acids, e.g.,hypoxanthine, 6-methyladenine, 5-Me pyrimidines, particularly5-methylcytosine (also referred to as 5-methyl-2′ deoxycytosine andoften referred to in the art as 5-Me-C), 5-hydroxymethylcytosine (HMC),glycosyl HMC and gentobiosyl HMC, as well as synthetic nucleobases,e.g., 2-aminoadenine, 2-(methylamino)adenine,2-(imidazolylalkyl)adenine, 2-(aminoalklyamino)adenine or otherheterosubstituted alkyladenines, 2-thiouracil, 2-thiothymine,5-bromouracil, 5-hydroxymethyluracil, 8-azaguanine, 7-deazaguanine, N6(6-aminohexyl)adenine, 2,6-diaminopurine; 5-ribosyluracil (Carlile(2014) Nature 515(7525): 143-6). Kornberg, A., DNA Replication, W. H.Freeman & Co., San Francisco, 1980, pp 75-′7′7; Gebeyehu (1987) Nucl.Acids Res. 15:4513). A “universal” base known in the art, e.g., inosine,can also be included. 5-Me-C substitutions have been shown to increasenucleic acid duplex stability by 0.6-1.2<0>C. (Sanghvi, Y. S., inCrooke, S. T. and Lebleu, B., eds., Antisense Research and Applications,CRC Press, Boca Raton, 1993, pp. 276-278) and are presently preferredbase substitutions.

It is not necessary for all positions in a given oligonucleotide to beuniformly modified, and in fact more than one of the aforementionedmodifications may be incorporated in a single oligonucleotide or even atwithin a single nucleoside within an oligonucleotide. In someembodiments, both the nucleobase and backbone may be modified to enhancestability and activity (El-Sagheer (2014) Chem Sci 5:253-259)

In some embodiments, both a sugar and an internucleoside linkage, i.e.,the backbone, of the nucleotide units are replaced with novel groups.The base units are maintained for hybridization with an appropriatenucleic acid target compound. One such oligomeric compound, anoligonucleotide mimetic that has been shown to have excellenthybridization properties, is referred to as a peptide nucleic acid(PNA). In PNA compounds, the sugar-backbone of an oligonucleotide isreplaced with an amide containing backbone, for example, anaminoethylglycine backbone. The nucleobases are retained and are bounddirectly or indirectly to aza nitrogen atoms of the amide portion of thebackbone. Representative United States patents that teach thepreparation of PNA compounds comprise, but are not limited to, U.S. Pat.Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is hereinincorporated by reference. Further teaching of PNA compounds can befound in Nielsen (1991) Science 254, 1497-1500; and Shi (2015).

Inhibitory nucleic acids can also include one or more nucleobase (oftenreferred to in the art simply as “base”) modifications or substitutions.As used herein, “unmodified” or “natural” nucleobases comprise thepurine bases adenine (A) and guanine (G), and the pyrimidine basesthymine (T), cytosine (C) and uracil (U). Modified nucleobases compriseother synthetic and natural nucleobases such as 5-methylcytosine(5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine,2-aminoadenine, 6-methyl and other alkyl derivatives of adenine andguanine, 2-propyl and other alkyl derivatives of adenine and guanine,2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil andcytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine andthymine, 5-uracil (pseudo-uracil), 4-thiouracil, 8-halo, 8-amino,8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines andguanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other5-substituted uracils and cytosines, 7-methylquanine and7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

Further, nucleobases comprise those disclosed in U.S. Pat. No.3,687,808, those disclosed in ‘The Concise Encyclopedia of PolymerScience And Engineering’, pages 858-859, Kroschwitz, J. I., ed. JohnWiley & Sons, 1990, those disclosed by Englisch et al., AngewandleChemie, International Edition’, 1991, 30, page 613, and those disclosedby Sanghvi, Y. S., Chapter 15, Antisense Research and Applications’,pages 289-302, Crooke, S. T. and Lebleu, B. ea., CRC Press, 1993.Certain of these nucleobases are particularly useful for increasing thebinding affinity of the oligomeric compounds of the invention. Theseinclude 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6substituted purines, comprising 2-aminopropyladenine, 5-propynyluraciland 5-propynylcytosine. 5-methylcytosine substitutions have been shownto increase nucleic acid duplex stability by 0.6-1.2<0>C (Sanghvi, Y.S., Crooke, S. T. and Lebleu, B., eds, ‘Antisense Research andApplications’, CRC Press, Boca Raton, 1993, pp. 276-278) and arepresently preferred base substitutions, even more particularly whencombined with 2′-O-methoxyethyl sugar modifications. Modifiednucleobases are described in U.S. Pat. No. 3,687,808, as well as U.S.Pat. Nos. 4,845,205; 5,130,302; 5,134,066; 5,175, 273; 5, 367,066;5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711;5,552,540; 5,587,469; 5,596,091; 5,614,617; 5,750,692, and 5,681,941,each of which is herein incorporated by reference.

In some embodiments, the inhibitory nucleic acids are chemically linkedto one or more moieties or conjugates that enhance the activity,cellular distribution, or cellular uptake of the oligonucleotide. Suchmoieties comprise but are not limited to, lipid moieties such as acholesterol moiety (Letsinger (1989) Proc. Natl. Acad. Sci. USA 86,6553-6556), cholic acid (Manoharan (1994) Bioorg. Med. Chem. Let. 4,1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan (1992)Ann. N. Y. Acad. Sci. 660, 306-309; Manoharan (1993) Bioorg. Med. Chem.Let. 3, 2765-2770), a thiocholesterol (Oberhauser (1992) Nucl. AcidsRes. 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecylresidues (Kabanov (1990) FEBS Lett. 259, 327-330; Svinarchuk (1993)Biochimie 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol ortriethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate(Manoharan (1995) Tetrahedron Lett. 36, 3651-3654; Shea (1990) Nucl.Acids Res.18, 3777-3783), a polyamine or a polyethylene glycol chain(Mancharan (1995) Nucleosides & Nucleotides 14, 969-973), or adamantaneacetic acid (Manoharan (1995) Tetrahedron Lett. 36, 3651-3654), apalmityl moiety (Mishra (1995) Biochim. Biophys. Acta 1264, 229-237), oran octadecylamine or hexylamino-carbonyl-t oxycholesterol moiety (Crooke(1996) J. Pharmacol. Exp. Ther. 277, 923-937). See also U.S. Pat. Nos.4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802;5,138,045; 5,414,077; 5,486, 603; 5,512,439; 5,578,718; 5,608,046;4,587,044; 4,605,735; 4,667,025; 4,762, 779; 4,789,737; 4,824,941;4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082, 830; 5,112,963;5,214,136; 5,082,830; 5,112,963; 5,214,136; 5, 245,022; 5,254,469;5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552;5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696;5,599,923; 5,599,928; 5,688,941, 8,865,677; 8,877,917 each of which isherein incorporated by reference.

These moieties or conjugates can include conjugate groups covalentlybound to functional groups such as primary or secondary hydroxyl groups.Conjugate groups of the invention include intercalators, reportermolecules, polyamines, polyamides, polyethylene glycols, polyethers,groups that enhance the pharmacodynamic properties of oligomers, andgroups that enhance the pharmacokinetic properties of oligomers. Typicalconjugate groups include cholesterols, lipids, phospholipids, biotin,phenazine, folate, phenanthridine, anthraquinone, acridine,fluoresceins, rhodamines, coumarins, and dyes. Groups that enhance thepharmacodynamic properties, in the context of this invention, includegroups that improve uptake, enhance resistance to degradation, and/orstrengthen sequence-specific hybridization with the target nucleic acid.Groups that enhance the pharmacokinetic properties, in the context ofthis invention, include groups that improve uptake, distribution,metabolism or excretion of the compounds of the present invention.Representative conjugate groups are disclosed in International PatentApplication No. PCT/US92/09196, filed Oct. 23, 1992, and U.S. Pat. No.6,287,860, which are incorporated herein by reference. Conjugatemoieties include, but are not limited to, lipid moieties such as acholesterol moiety, cholic acid, a thioether, e.g., hexyl-5-tritylthiol,a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecylresidues, a phospholipid, e.g., di-hexadecyl-rac-glycerol ortriethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, apolyamine or a polyethylene glycol chain, or adamantane acetic acid, apalmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety. See, e.g., U.S. Pat. Nos. 4,828,979; 4,948,882;5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717,5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045;5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044;4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263;4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136;5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506;5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723;5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552;5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696;5,599,923; 5,599,928 and 5,688,941.

The inhibitory nucleic acids useful in the present methods aresufficiently complementary to the target lncRNA, i.e., hybridizesufficiently well and with sufficient specificity, to give the desiredeffect. “Complementary” in this context refers to the capacity forpairing, through hydrogen bonding, between two sequences comprisingnaturally or non-naturally occurring bases or analogs thereof. Forexample, if a base at one position of an inhibitory nucleic acid iscapable of hydrogen bonding with a base at the corresponding position ofa lncRNA, then the bases are considered to be complementary to eachother at that position. 100% complementarity is not required.

In some embodiments, the location on a target lncRNA to which aninhibitory nucleic acids hybridizes is defined as a target region towhich a protein binding partner binds. These regions can be identifiedby reviewing the data submitted herewith in Appendix I and identifyingregions that are enriched in the dataset; these regions are likely toinclude the protein binding sequences. Routine methods can be used todesign an inhibitory nucleic acid that binds to this sequence withsufficient specificity. In some embodiments, the methods include usingbioinformatics methods known in the art to identify regions of secondarystructure, e.g., one, two, or more stem-loop structures, or pseudoknots,and selecting those regions to target with an inhibitory nucleic acid.

While the specific sequences of certain exemplary target segments areset forth herein, one of skill in the art will recognize that theseserve to illustrate and describe particular embodiments within the scopeof the present invention. Additional target segments are readilyidentifiable by one having ordinary skill in the art in view of thisdisclosure. Target segments 5-500 nucleotides in length comprising astretch of at least five (5) consecutive nucleotides within the proteinbinding region, or immediately adjacent thereto, are considered to besuitable for targeting as well. Target segments can include sequencesthat comprise at least the 5 consecutive nucleotides from the5′-terminus of one of the protein binding regions (the remainingnucleotides being a consecutive stretch of the same RNA beginningimmediately upstream of the 5′-terminus of the binding segment andcontinuing until the inhibitory nucleic acid contains about 5 to about100 nucleotides). Similarly preferred target segments are represented byRNA sequences that comprise at least the 5 consecutive nucleotides fromthe 3′-terminus of one of the illustrative preferred target segments(the remaining nucleotides being a consecutive stretch of the samelncRNA beginning immediately downstream of the 3′-terminus of the targetsegment and continuing until the inhibitory nucleic acid contains about5 to about 100 nucleotides). One having skill in the art armed with thesequences provided herein will be able, without undue experimentation,to identify further preferred protein binding regions to target.

Once one or more target regions, segments or sites have been identified,inhibitory nucleic acid compounds are chosen that are sufficientlycomplementary to the target, i.e., that hybridize sufficiently well andwith sufficient specificity (i.e., do not substantially bind to othernon-target RNAs), to give the desired effect.

Making and Using Inhibitory Nucleic Acids

The inhibitory nucleic acids used to practice the methods describedherein, whether RNA, cDNA, genomic DNA, vectors, viruses or hybridsthereof, can be isolated from a variety of sources, geneticallyengineered, amplified, and/or expressed, generated recombinantly orsynthetically by well-known chemical synthesis techniques, as describedin, e.g., Adams (1983) J. Am. Chem. Soc. 105:661; Belousov (1997)Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol. Med.19:373-380; Blommers (1994) Biochemistry 33:7886-7896; Narang (1979)Meth. Enzymol. 68:90; Brown (1979) Meth. Enzymol. 68:109; Beaucage(1981) Tetra. Lett. 22:1859; Maier (2000) Org Lett 2(13):1819-1822;Egeland (2005) Nucleic Acids Res 33(14):e125; Krotz (2005) Pharm DevTechnol 10(2):283-90 U.S. Pat. No. 4,458,066. Recombinant nucleic acidsequences can be individually isolated or cloned and tested for adesired activity. Any recombinant expression system can be used,including e.g. in vitro bacterial, fungal, mammalian, yeast, insect orplant cell expression systems.

Nucleic acid sequences of the invention can be inserted into deliveryvectors and expressed from transcription units within the vectors. Therecombinant vectors can be DNA plasmids or viral vectors. Generation ofthe vector construct can be accomplished using any suitable geneticengineering techniques well known in the art, including, withoutlimitation, the standard techniques of PCR, oligonucleotide synthesis,restriction endonuclease digestion or “seamless cloning”, ligation,transformation, plasmid purification, and DNA sequencing, for example asdescribed in Sambrook et al. “Molecular Cloning: A Laboratory Manual.”(1989)), Coffin et al. (Retroviruses. (1997)) and “RNA Viruses: APractical Approach” (Alan J. Cann, Ed., Oxford University Press,(2000)). “Seamless cloning” allows joining of multiple fragments ofnucleic acids in a single, isothermal reaction (Gibson (2009) NatMethods 6:343-345; Werner (2012) Bioeng Bugs 3:38-43; Sanjana (2012) NatProtoc 7:171-192). As will be apparent to one of ordinary skill in theart, a variety of suitable vectors are available for transferringnucleic acids of the invention into cells. The selection of anappropriate vector to deliver nucleic acids and optimization of theconditions for insertion of the selected expression vector into thecell, are within the scope of one of ordinary skill in the art withoutthe need for undue experimentation. Viral vectors comprise a nucleotidesequence having sequences for the production of recombinant virus in apackaging cell. Viral vectors expressing nucleic acids of the inventioncan be constructed based on viral backbones including, but not limitedto, a retrovirus, lentivirus, adenovirus, adeno-associated virus, poxvirus or alphavirus (Warnock (2011) Methods in Molecular Biology737:1-25). The recombinant vectors capable of expressing the nucleicacids of the invention can be delivered as described herein, and persistin target cells (e.g., stable transformants).

This can be achieved, for example, by administering an inhibitorynucleic acid, e.g., antisense oligonucleotides complementary to p40and/or CD5L. Other inhibitory nucleic acids for use in practicing themethods described herein and that are complementary to p40 and/or CD5Lcan be those which inhibit post-transcriptional processing of p40 orCD5L, such as inhibitors of mRNA translation (antisense), agents of RNAinterference (RNAi), catalytically active RNA molecules (ribozymes), andRNAs that bind proteins and other molecular ligands (aptamers).Additional methods exist to inhibit endogenous microRNA (miRNA) activitythrough the use of antisense-miRNA oligonucleotides (antagomirs) and RNAcompetitive inhibitors or decoys (miRNA sponges).

For further disclosure regarding inhibitory nucleic acids, please seeUS2010/0317718 (antisense oligos); US2010/0249052 (double-strandedribonucleic acid (dsRNA)); US2009/0181914 and US2010/0234451 (LNAs);US2007/0191294 (siRNA analogues); US2008/0249039 (modified siRNA); andWO2010/129746 and WO2010/040112 (inhibitory nucleic acids).

Antisense

In some embodiments, the inhibitory nucleic acids are antisenseoligonucleotides. Antisense oligonucleotides are typically designed toblock expression of a DNA or RNA target by binding to the target andhalting expression at the level of transcription, translation, orsplicing. Antisense oligonucleotides of the present invention arecomplementary nucleic acid sequences designed to hybridize understringent conditions to p40 and/or CD5L. Thus, oligonucleotides arechosen that are sufficiently complementary to the target, i.e., thathybridize sufficiently well and with sufficient specificity, to give thedesired effect, while striving to avoid significant off-target effectsi.e. must not directly bind to, or directly significantly affectexpression levels of, transcripts other than the intended target. Theoptimal length of the antisense oligonucleotide may very but it shouldbe as short as possible while ensuring that its target sequence isunique in the transcriptome i.e. antisense oligonucleotides may be asshort as 12-mers (Seth (2009) J Med Chem 52:10-13) to 18-22 nucleotidesin length.

In the context of this invention, hybridization means hydrogen bonding,which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogenbonding, between complementary nucleoside or nucleotide bases. Forexample, adenine and thymine are complementary nucleobases which pairthrough the formation of hydrogen bonds. Complementary, as used herein,refers to the capacity for precise pairing between two nucleotides. Forexample, if a nucleotide at a certain position of an oligonucleotide iscapable of hydrogen bonding with a nucleotide at the same position of aDNA or RNA molecule, then the oligonucleotide and the DNA or RNA areconsidered to be complementary to each other at that position. Theoligonucleotide and the DNA or RNA are complementary to each other whena sufficient number of corresponding positions in each molecule areoccupied by nucleotides which can hydrogen bond with each other. Thus,“specifically hybridizable” and “complementary” are terms which are usedto indicate a sufficient degree of complementarity or precise pairingsuch that stable and specific binding occurs between the oligonucleotideand the DNA or RNA target.

It is understood in the art that a complementary nucleic acid sequenceneed not be 100% complementary to that of its target nucleic acid to bespecifically hybridisable. A complementary nucleic acid sequence of theinvention is specifically hybridisable when binding of the sequence tothe target DNA or RNA molecule interferes with the normal function ofthe target DNA or RNA to cause a loss of activity, and there is asufficient degree of complementarity to avoid non-specific binding ofthe sequence to non-target sequences under conditions in which specificbinding is desired, i.e., under physiological conditions in the case ofin vivo assays or therapeutic treatment, and in the case of in vitroassays, under conditions in which the assays are performed undersuitable conditions of stringency. The antisense oligonucleotides usefulin the methods described herein have at least 80% sequencecomplementarity to a target region within the target nucleic acid, e.g.,90%, 95%, or 100% sequence complementarity to the target region withinp40 or CD5L (e.g., a target region comprising the seed sequence).Percent complementarity of an antisense compound with a region of atarget nucleic acid can be determined routinely using basic localalignment search tools (BLAST programs) (Altschul (1990) J. Mol. Biol.215, 403-410; Zhang and Madden (1997) Genome Res. 7, 649-656). Thespecificity of an antisense oligonucleotide can also be determinedroutinely using BLAST program against the entire genome of a givenspecies

For example, stringent salt concentration will ordinarily be less thanabout 750 mM NaCl and 75 mM trisodium citrate, preferably less thanabout 500 mM NaCl and 50 mM trisodium citrate, and more preferably lessthan about 250 mM NaCl and 25 mM trisodium citrate. Low stringencyhybridization can be obtained in the absence of organic solvent, e.g.,formamide, while high stringency hybridization can be obtained in thepresence of at least about 35% formamide, and more preferably at leastabout 50% formamide. Stringent temperature conditions will ordinarilyinclude temperatures of at least about 30° C., more preferably of atleast about 37° C., and most preferably of at least about 42° C. Varyingadditional parameters, such as hybridization time, the concentration ofdetergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion orexclusion of carrier DNA, are well known to those skilled in the art.Various levels of stringency are accomplished by combining these variousconditions as needed. In a preferred embodiment, hybridization willoccur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. Ina more preferred embodiment, hybridization will occur at 37° C. in 500mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 μg/mldenatured salmon sperm DNA (ssDNA). In a most preferred embodiment,hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodiumcitrate, 1% SDS, 50% formamide, and 200 μg/ml ssDNA. Useful variationson these conditions will be readily apparent to those skilled in theart. For most applications, washing steps that follow hybridization willalso vary in stringency. Wash stringency conditions can be defined bysalt concentration and by temperature. As above, wash stringency can beincreased by decreasing salt concentration or by increasing temperature.For example, stringent salt concentration for the wash steps willpreferably be less than about 30 mM NaCl and 3 mM trisodium citrate, andmost preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.Stringent temperature conditions for the wash steps will ordinarilyinclude a temperature of at least about 25° C., more preferably of atleast about 42° C., and even more preferably of at least about 68° C. Ina preferred embodiment, wash steps will occur at 25° C. in 30 mM NaCl, 3mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, washsteps will occur at 42° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and0.1% SDS. In a more preferred embodiment, wash steps will occur at 68°C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additionalvariations on these conditions will be readily apparent to those skilledin the art. Hybridization techniques are well known to those skilled inthe art and are described, for example, in Benton and Davis (Science196:180, 1977); Grunstein and Hogness (Proc. Natl. Acad. Sci., USA72:3961, 1975); Ausubel et al. (Current Protocols in Molecular Biology,Wiley Interscience, New York, 2001); Berger and Kimmel (Guide toMolecular Cloning Techniques, 1987, Academic Press, New York); andSambrook et al., Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratory Press, New York, Hilario (2007) Methods Mol Biol353:27-38.

Inhibitory nucleic acids for use in the methods described herein caninclude one or more modifications, e.g., be stabilized againstnucleolytic degradation such as by the incorporation of a modification,e.g., a nucleotide modification. For example, inhibitory nucleic acidscan include a phosphorothioate at least the first, second, or thirdinternucleotide linkage at the 5′ or 3′ end of the nucleotide sequence.As another example, inhibitory nucleic acids can include a 2′-modifiednucleotide, e.g., a 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl,2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP),2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl(2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), or2′-O—N-methylacetamido (2′-O-NMA). As another example, the inhibitorynucleic acids can include at least one 2′-O-methyl-modified nucleotide,and in some embodiments, all of the nucleotides include a 2′-O-methylmodification.

MODIFICATIONS

Chemical modifications, particularly the use of locked nucleic acids(LNAs) (Okiba (1997) Tetrahedron Lett 39:5401-5404; Singh (1998) ChemCommun 4:455-456), 2′-O-methoxyethyl (2′-O-MOE) (Martin (1995) Helv ChimActa 78:486-504; You (2006) Nucleic Acids Res 34(8):e60; Owczarzy (2011)Biochem 50(43):9352-9367), constrained ethyl BNA (cET) (Murray (2012)Nucleic Acids Res 40: 6135-6143), and gapmer oligonucleotides, whichcontain 2-5 chemically modified nucleotides (LNA, 2′-O-MOE RNA or cET)at each terminus flanking a central 5-10 base “gap” of DNA (Monia (1993)J Biol Chem 268:14514-14522; Wahlestedt (2000) PNAS 97:5633-5638),improve antisense oligonucleotide binding affinity for the target RNA,which increases the steric block efficiency. Antisense oligos thathybridize to p40 or CD5L, can be identified through experimentation.

Techniques for the manipulation of inhibitory nucleic acids, such as,e.g., subcloning, labeling probes (e.g., random-primer labeling usingKlenow polymerase, nick translation, amplification), sequencing,hybridization and the like are well described in the scientific andpatent literature, see, e.g., Sambrook et al., Molecular Cloning; ALaboratory Manual 3d ed. (2001); Current Protocols in Molecular Biology,Ausubel et al., eds. (John Wiley & Sons, Inc., New York 2010); Kriegler,Gene Transfer and Expression: A Laboratory Manual (1990); LaboratoryTechniques In Biochemistry And Molecular Biology: Hybridization WithNucleic Acid Probes, Part I. Theory and Nucleic Acid Preparation,Tijssen, ed. Elsevier, N.Y. (1993).

Modified Bases/Locked Nucleic Acids (LNAs)

In some embodiments, the inhibitory nucleic acids are “locked,” i.e.,comprise nucleic acid analogues in which the ribose ring is “locked” bya methylene bridge connecting the 2′-O atom and the 4′-C atom (see,e.g., Kaupinnen (2005) Drug Disc. Today 2(3):287-290; Koshkin (1998) J.Am. Chem. Soc. 120(50):13252-13253). For additional modifications see US20100004320, US 20090298916, and US 20090143326.

siRNA/shRNA

In some embodiments, the nucleic acid sequence that is complementary top40 or CD5L can be an interfering RNA, including but not limited to asmall interfering RNA (“siRNA”) or a small hairpin RNA (“shRNA”).Methods for constructing interfering RNAs are well known in the art. Forexample, the interfering RNA can be assembled from two separateoligonucleotides, where one strand is the sense strand and the other isthe antisense strand, wherein the antisense and sense strands areself-complementary (i.e., each strand comprises nucleotide sequence thatis complementary to nucleotide sequence in the other strand; such aswhere the antisense strand and sense strand form a duplex or doublestranded structure); the antisense strand comprises nucleotide sequencethat is complementary to a nucleotide sequence in a target nucleic acidmolecule or a portion thereof (i.e., an undesired gene) and the sensestrand comprises nucleotide sequence corresponding to the target nucleicacid sequence or a portion thereof. Alternatively, interfering RNA isassembled from a single oligonucleotide, where the self-complementarysense and antisense regions are linked by means of nucleic acid based ornon-nucleic acid-based linker(s). The interfering RNA can be apolynucleotide with a duplex, asymmetric duplex, hairpin or asymmetrichairpin secondary structure, having self-complementary sense andantisense regions, wherein the antisense region comprises a nucleotidesequence that is complementary to nucleotide sequence in a separatetarget nucleic acid molecule or a portion thereof and the sense regionhaving nucleotide sequence corresponding to the target nucleic acidsequence or a portion thereof. The interfering can be a circularsingle-stranded polynucleotide having two or more loop structures and astem comprising self-complementary sense and antisense regions, whereinthe antisense region comprises nucleotide sequence that is complementaryto nucleotide sequence in a target nucleic acid molecule or a portionthereof and the sense region having nucleotide sequence corresponding tothe target nucleic acid sequence or a portion thereof, and wherein thecircular polynucleotide can be processed either in vivo or in vitro togenerate an active siRNA molecule capable of mediating RNA interference.RNA interference may cause translational repression and degradation oftarget mRNAs with imperfect complementarity or sequence-specificcleavage of perfectly complementary mRNAs.

In some embodiments, the interfering RNA coding region encodes aself-complementary RNA molecule having a sense region, an antisenseregion and a loop region. Such an RNA molecule when expressed desirablyforms a “hairpin” structure, and is referred to herein as an “shRNA.”The loop region is generally between about 2 and about 10 nucleotides inlength. In some embodiments, the loop region is from about 6 to about 9nucleotides in length. In some embodiments, the sense region and theantisense region are between about 15 and about 20 nucleotides inlength. Following post-transcriptional processing, the small hairpin RNAis converted into a siRNA by a cleavage event mediated by the enzymeDicer, which is a member of the RNase III family. The siRNA is thencapable of inhibiting the expression of a gene with which it shareshomology. After the siRNA has cleaved its target, it is released fromthat RNA to search for another target and can repeatedly bind and cleavenew targets (Brummelkamp (2002) Science 296:550-553; Lee (2002) NatureBiotechnol., 20, 500-505; Miyagishi and Taira (2002) Nature Biotechnol20:497-500; Paddison (2002) Genes & Dev. 16:948-958; Paul (2002) NatureBiotechnol 20, 505-508; Sui (2002) Proc. Natl. Acad. Sd. USA 99(6),5515-5520; Yu (2002) Proc Natl Acad Sci USA 99:6047-6052; Peer andLieberman (2011) Gen Ther 18, 1127-1133).

The target RNA cleavage reaction guided by siRNAs is highly sequencespecific. In general, siRNA containing a nucleotide sequences identicalto a portion of the target nucleic acid are preferred for inhibition.However, 100% sequence identity between the siRNA and the target gene isnot required to practice the present invention. Thus the invention hasthe advantage of being able to tolerate sequence variations that mightbe expected due to genetic mutation, strain polymorphism, orevolutionary divergence. For example, siRNA sequences with insertions,deletions, and single point mutations relative to the target sequencehave also been found to be effective for inhibition. Alternatively,siRNA sequences with nucleotide analog substitutions or insertions canbe effective for inhibition. In general the siRNAs must retainspecificity for their target, i.e., must not directly bind to, ordirectly significantly affect expression levels of, transcripts otherthan the intended target. shRNAs that are constitutively expressed formpromoters can ensure long-term gene silencing. Most methods commonlyused for delivery of siRNAs rely on commonly used techniques forintroducing an exogenous nucleic acid into a cell including calciumphosphate or calcium chloride precipitation, microinjection,DEAE-dextrin-mediated transfection, lipofection, commercially availablecationic polymers and lipids and cell-penetrating peptides,electroporation or stable nucleic acid-lipid particles (SNALPs), all ofwhich are routine in the art. siRNAs can also be conjugated to smallmolecules to direct binding to cell-surface receptors, such ascholesterol (Wolfrum (2007) Nat Biotechnol 25:1149-1157),alpha-tocopherol (Nishina (2008) Mol Ther 16:734-40), lithocholic acidor lauric acid (Lorenz (2004) Bioorg Med Chem Lett 14:4975-4977),polyconjugates (Rozema (2007) PNAS 104:12982-12987). A variation ofconjugated siRNAs are aptamer-siRNA chimeras (McNamara (2006) NatBiotechnol 24:1005-1015; Dassie (2009) Nat Biotechnol 27:839-849) andsiRNA-fusion protein complexes, which is composed of a targetingpeptide, such as an antibody fragment that recognizes a cell-surfacereceptor or ligand, linked to an RNA-binding peptide that can becomplexed to siRNAs for targeted systemic siRNA delivery (Yao (2011) SciTransl Med 4(130):130ra48.

Ribozymes

Trans-cleaving enzymatic nucleic acid molecules can also be used; theyhave shown promise as therapeutic agents for human disease (Usman &McSwiggen, (1995) Ann. Rep. Med. Chem. 30, 285-294; Christoffersen andMarr (1995) J. Med. Chem. 38, 2023-2037; Weng (2005) Mol Cancer Ther 4,948-955; Armado (2004) Hum Gene Ther 15, 251-262; Macpherson (2005) JGene Med 7,552-564; Muhlbacher (2010) Curr Opin Pharamacol 10(5):551-6).Enzymatic nucleic acid molecules can be designed to cleave specific p40and/or CD5L targets within the background of cellular RNA. Such acleavage event renders the p40 and/or CD5L non-functional.

In general, enzymatic nucleic acids with RNA cleaving activity act byfirst binding to a target RNA. Such binding occurs through the targetbinding portion of an enzymatic nucleic acid which is held in closeproximity to an enzymatic portion of the molecule that acts to cleavethe target RNA. Thus, the enzymatic nucleic acid first recognizes andthen binds a target RNA through complementary base pairing, and oncebound to the correct site, acts enzymatically to cut the target RNA.Strategic cleavage of such a target RNA will destroy its ability todirect synthesis of an encoded protein. After an enzymatic nucleic acidhas bound and cleaved its RNA target, it is released from that RNA tosearch for another target and can repeatedly bind and cleave newtargets.

Several approaches such as in vitro selection (evolution) strategies(Orgel (1979) Proc. R. Soc. London B 205, 435) have been used to evolvenew nucleic acid catalysts with improved properties, new functions andcapable of catalyzing a variety of reactions, such as cleavage andligation of phosphodiester linkages and amide linkages, (Joyce (1989)Gene 82, 83-87; Beaudry (1992) Science 257, 635-641; Joyce (1992)Scientific American 267, 90-97; Breaker (1994) TIBTECH 12, 268; Bartel(1993) Science 261:1411-1418; Szostak (1993) MS 17, 89-93; Kumar (1995)FASEB J. 9, 1183; Breaker (1996) Curr. Op. Biotech. 1, 442; Scherer(2003) Nat Biotechnol 21, 1457-1465; Berens (2015) Curr. Op. Biotech.31, 10-15). Ribozymes can also be engineered to be allostericallyactivated by effector molecules (riboswitches, Liang (2011) Mol Cell 43,915-926; Wieland (2010) Chem Biol 17, 236-242; U.S. Pat. No. 8,440,810).The development of ribozymes that are optimal for catalytic activitywould contribute significantly to any strategy that employs RNA-cleavingribozymes for the purpose of regulating gene expression. The most commonribozyme therapeutics are derived from either hammerhead orhairpin/paperclip motifs. The hammerhead ribozyme, for example,functions with a catalytic rate (kcat) of about 1 min-1 in the presenceof saturating (10 rnM) concentrations of Mg2+ cofactor. An artificial“RNA ligase” ribozyme has been shown to catalyze the correspondingself-modification reaction with a rate of about 100 min-1. In addition,it is known that certain modified hammerhead ribozymes that havesubstrate binding arms made of DNA catalyze RNA cleavage with multipleturn-over rates that approach 100 min-1. Ribozymes can be delivered totarget cells in RNA form or can be transcribed from vectors. Due to poorstability of fully-RNA ribozymes, ribozymes often require chemicalmodification, such as, 5′-PS backbone linkage, 2′-O-Me,2′-deoxy-2′-C-allyl uridine, and terminal inverted 3′-3′ deoxyabasicnucleotides (Kobayashi (2005) Cancer Chemother Pharmacol 56, 329-336).

CRISPR/Cas, TALENs, and Zinc Finger Nucleases (ZFNs)

As mentioned above, some embodiments comprise methods gene targetingand/or genome editing. Such methods are useful, e.g., in the context ofdecreasing protein expression in vivo and/or modifying cells in vitro(e.g., in the context of adoptive cell therapies). In some embodiments,genes are targeting and/or edited using DNA binding proteins.

In some embodiments, the methods described herein include the use oftranscription activator effector-like nucleases (TALENs), ClusteredRegularly Interspaced Short Palindromic Repeats (CRISPR) Cas RNA-guidednucleases (RGNs), or zinc finger nucleases (ZFNs) to inhibit expressionof CD5L and/or p40. In these methods, engineered nucleases are used tospecifically target and disrupt expression of CD5L and/or p40. Methodsfor using CRISPR, TALENs, and ZFNs are well known in the art.

Gene Targeting and Genome Editing

As mentioned above, some embodiments comprise methods gene targetingand/or genome editing. Such methods are useful, e.g., in the context ofdecreasing protein expression in vivo and/or modifying cells in vitro(e.g., in the context of adoptive cell therapies). In some embodiments,genes are targeting and/or edited using DNA binding proteins.

In certain embodiments, the DNA binding protein is a (endo)nuclease or avariant thereof having altered or modified activity (i.e. a modifiednuclease, as described herein elsewhere). In certain embodiments, saidnuclease is a targeted or site-specific or homing nuclease or a variantthereof having altered or modified activity. In certain embodiments,said nuclease or targeted/site-specific/homing nuclease is, comprises,consists essentially of, or consists of a (modified) CRISPR/Cas systemor complex, a (modified) Cas protein, a (modified) zinc finger, a(modified) zinc finger nuclease (ZFN), a (modified) transcriptionfactor-like effector (TALE), a (modified) transcription factor-likeeffector nuclease (TALEN), or a (modified) meganuclease. In certainembodiments, said (modified) nuclease or targeted/site-specific/homingnuclease is, comprises, consists essentially of, or consists of a(modified) RNA-guided nuclease. As used herein, the term “Cas” generallyrefers to a (modified) effector protein of the CRISPR/Cas system orcomplex, and can be without limitation a (modified) Cas9, or otherenzymes such as Cpf1, The term “Cas” may be used herein interchangeablywith the terms “CRISPR” protein, “CRISPR/Cas protein”, “CRISPReffector”, “CRISPR/Cas effector”, “CRISPR enzyme”, “CRISPR/Cas enzyme”and the like, unless otherwise apparent, such as by specific andexclusive reference to Cas9. It is to be understood that the term“CRISPR protein” may be used interchangeably with “CRISPR enzyme”,irrespective of whether the CRISPR protein has altered, such asincreased or decreased (or no) enzymatic activity, compared to the wildtype CRISPR protein. Likewise, as used herein, in certain embodiments,where appropriate and which will be apparent to the skilled person, theterm “nuclease” may refer to a modified nuclease wherein catalyticactivity has been altered, such as having increased or decreasednuclease activity, or no nuclease activity at all, as well as nickaseactivity, as well as otherwise modified nuclease as defined hereinelsewhere, unless otherwise apparent, such as by specific and exclusivereference to unmodified nuclease.

As used herein, the term “targeting” of a selected nucleic acid sequencemeans that a nuclease or nuclease complex is acting in a nucleotidesequence specific manner. For instance, in the context of the CRISPR/Cassystem, the guide RNA is capable of hybridizing with a selected nucleicacid sequence. As uses herein, “hybridization” or “hybridizing” refersto a reaction in which one or more polynucleotides react to form acomplex that is stabilized via hydrogen bonding between the bases of thenucleotide residues. The hydrogen bonding may occur by Watson Crick basepairing, Hoogstein binding, or in any other sequence specific manner.The complex may comprise two strands forming a duplex structure, threeor more strands forming a multi stranded complex, a singleself-hybridizing strand, or any combination of these. A hybridizationreaction may constitute a step in a more extensive process, such as theinitiation of PGR, or the cleavage of a polynucleotide by an enzyme. Asequence capable of hybridizing with a given sequence is referred to asthe “complement” of the given sequence.

In certain embodiments, the DNA binding protein is a (modified)transcription activator-like effector nuclease (TALEN) system.Transcription activator-like effectors (TALEs) can be engineered to bindpractically any desired DNA sequence. Exemplary methods of genomeediting using the TALEN system can be found for example in Cermak T.Doyle E L. Christian M. Wang L. Zhang Y. Schmidt C, et al. Efficientdesign and assembly of custom TALEN and other TAL effector-basedconstructs for DNA targeting. Nucleic Acids Res. 2011; 39:e82; Zhang F.Cong L. Lodato S. Kosuri S. Church G M. Arlotta P Efficient constructionof sequence-specific TAL effectors for modulating mammaliantranscription. Nat Biotechnol. 2011; 29:149-153 and U.S. Pat. Nos.8,450,471, 8,440,431 and 8,440,432, all of which are specificallyincorporated by reference. By means of further guidance, and withoutlimitation, naturally occurring TALEs or “wild type TALEs” are nucleicacid binding proteins secreted by numerous species of proteobacteria.TALE polypeptides contain a nucleic acid binding domain composed oftandem repeats of highly conserved monomer polypeptides that arepredominantly 33, 34 or 35 amino acids in length and that differ fromeach other mainly in amino acid positions 12 and 13. In advantageousembodiments the nucleic acid is DNA. As used herein, the term“polypeptide monomers”, or “TALE monomers” will be used to refer to thehighly conserved repetitive polypeptide sequences within the TALEnucleic acid binding domain and the term “repeat variable di-residues”or “RVD” will be used to refer to the highly variable amino acids atpositions 12 and 13 of the polypeptide monomers. As provided throughoutthe disclosure, the amino acid residues of the RVD are depicted usingthe IUPAC single letter code for amino acids. A general representationof a TALE monomer which is comprised within the DNA binding domain isX1-11-(X12X13)-X14-33 or 34 or 35, where the subscript indicates theamino acid position and X represents any amino acid. X12X13 indicate theRVDs. In some polypeptide monomers, the variable amino acid at position13 is missing or absent and in such polypeptide monomers, the RVDconsists of a single amino acid. In such cases the RVD may bealternatively represented as X*, where X represents X12 and (*)indicates that X13 is absent. The DNA binding domain comprises severalrepeats of TALE monomers and this may be represented as(X1-11-(X12X13)-X14-33 or 34 or 35)z, where in an advantageousembodiment, z is at least 5 to 40. In a further advantageous embodiment,z is at least 10 to 26. The TALE monomers have a nucleotide bindingaffinity that is determined by the identity of the amino acids in itsRVD. For example, polypeptide monomers with an RVD of NI preferentiallybind to adenine (A), polypeptide monomers with an RVD of NGpreferentially bind to thymine (T), polypeptide monomers with an RVD ofHD preferentially bind to cytosine (C) and polypeptide monomers with anRVD of NN preferentially bind to both adenine (A) and guanine (G). Inyet another embodiment of the invention, polypeptide monomers with anRVD of IG preferentially bind to T. Thus, the number and order of thepolypeptide monomer repeats in the nucleic acid binding domain of a TALEdetermines its nucleic acid target specificity. In still furtherembodiments of the invention, polypeptide monomers with an RVD of NSrecognize all four base pairs and may bind to A, T, G or C. Thestructure and function of TALEs is further described in, for example,Moscou et al., Science 326:1501 (2009); Boch et al., Science326:1509-1512 (2009); and Zhang et al., Nature Biotechnology 29:149-153(2011), each of which is incorporated by reference in its entirety.

In certain embodiments, the nucleic acid modification is effected by a(modified) zinc-finger nuclease (ZFN) system. The ZFN system usesartificial restriction enzymes generated by fusing a zinc fingerDNA-binding domain to a DNA-cleavage domain that can be engineered totarget desired DNA sequences. Exemplary methods of genome editing usingZFNs can be found for example in U.S. Pat. Nos. 6,534,261, 6,607,882,6,746,838, 6,794,136, 6,824,978, 6,866,997, 6,933,113, 6,979,539,7,013,219, 7,030,215, 7,220,719, 7,241,573, 7,241,574, 7,585,849,7,595,376, 6,903,185, and 6,479,626, all of which are specificallyincorporated by reference. By means of further guidance, and withoutlimitation, artificial zinc-finger (ZF) technology involves arrays of ZFmodules to target new DNA-binding sites in the genome. Each fingermodule in a ZF array targets three DNA bases. A customized array ofindividual zinc finger domains is assembled into a ZF protein (ZFP).ZFPs can comprise a functional domain. The first synthetic zinc fingernucleases (ZFNs) were developed by fusing a ZF protein to the catalyticdomain of the Type IIS restriction enzyme Fokl. (Kim, Y. G. et al.,1994, Chimeric restriction endonuclease, Proc. Natl. Acad. Sci. U.S.A.91, 883-887; Kim, Y. G. et al., 1996, Hybrid restriction enzymes: zincfinger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. U.S.A.93, 1156-1160). Increased cleavage specificity can be attained withdecreased off target activity by use of paired ZFN heterodimers, eachtargeting different nucleotide sequences separated by a short spacer.(Doyon, Y. et al., 2011, Enhancing zinc-finger-nuclease activity withimproved obligate heterodimeric architectures. Nat. Methods 8, 74-79).ZFPs can also be designed as transcription activators and repressors andhave been used to target many genes in a wide variety of organisms.

In certain embodiments, the nucleic acid modification is effected by a(modified) meganuclease, which are endodeoxyribonucleases characterizedby a large recognition site (double-stranded DNA sequences of 12 to 40base pairs). Exemplary method for using meganucleases can be found inU.S. Pat. Nos. 8,163,514; 8,133,697; 8,021,867; 8,119,361; 8,119,381;8,124,369; and 8,129,134, which are specifically incorporated byreference.

In certain embodiments, the nucleic acid modification is effected by a(modified) CRISPR/Cas complex or system. With respect to generalinformation on CRISPR/Cas Systems, components thereof, and delivery ofsuch components, including methods, materials, delivery vehicles,vectors, particles, and making and using thereof, including as toamounts and formulations, as well as Cas9CRISPR/Cas-expressingeukaryotic cells, Cas-9 CRISPR/Cas expressing eukaryotes, such as amouse, reference is made to: U.S. Pat. Nos. 8,999,641, 8,993,233,8,697,359, 8,771,945, 8,795,965, 8,865,406, 8,871,445, 8,889,356,8,889,418, 8,895,308, 8,906,616, 8,932,814, 8,945,839, 8,993,233 and8,999,641; US Patent Publications US 2014-0310830 (U.S. application Ser.No. 14/105,031), US 2014-0287938 A1 (U.S. application Ser. No.14/213,991), US 2014-0273234 A1 (U.S. application Ser. No. 14/293,674),US2014-0273232 A1 (U.S. application Ser. No. 14/290,575), US2014-0273231 (U.S. application Ser. No. 14/259,420), US 2014-0256046 A1(U.S. application Ser. No. 14/226,274), US 2014-0248702 A1 (U.S.application Ser. No. 14/258,458), US 2014-0242700 A1 (U.S. applicationSer. No. 14/222,930), US 2014-0242699 A1 (U.S. application Ser. No.14/183,512), US 2014-0242664 A1 (U.S. application Ser. No. 14/104,990),US 2014-0234972 A1 (U.S. application Ser. No. 14/183,471), US2014-0227787 A1 (U.S. application Ser. No. 14/256,912), US 2014-0189896A1 (U.S. application Ser. No. 14/105,035), US 2014-0186958 (U.S.application Ser. No. 14/105,017), US 2014-0186919 A1 (U.S. applicationSer. No. 14/104,977), US 2014-0186843 A1 (U.S. application Ser. No.14/104,900), US 2014-0179770 A1 (U.S. application Ser. No. 14/104,837)and US 2014-0179006 A1 (U.S. application Ser. No. 14/183,486), US2014-0170753 (U.S. application Ser. No. 14/183,429); US 2015-0184139(U.S. application Ser. No. 14/324,960); Ser. No. 14/054,414 EuropeanPatent Applications EP 2 771 468 (EP13818570.7), EP 2 764 103(EP13824232.6), and EP 2 784 162 (EP14170383.5); and PCT PatentPublications WO 2014/093661 (PCT/US2013/074743), WO 2014/093694(PCT/US2013/074790), WO 2014/093595 (PCT/US2013/074611), WO 2014/093718(PCT/US2013/074825), WO 2014/093709 (PCT/US2013/074812), WO 2014/093622(PCT/US2013/074667), WO 2014/093635 (PCT/US2013/074691), WO 2014/093655(PCT/US2013/074736), WO 2014/093712 (PCT/US2013/074819), WO 2014/093701(PCT/US2013/074800), WO 2014/018423 (PCT/US2013/051418), WO 2014/204723(PCT/US2014/041790), WO 2014/204724 (PCT/US2014/041800), WO 2014/204725(PCT/US2014/041803), WO 2014/204726 (PCT/US2014/041804), WO 2014/204727(PCT/US2014/041806), WO 2014/204728 (PCT/US2014/041808), WO 2014/204729(PCT/US2014/041809), WO 2015/089351 (PCT/US2014/069897), WO 2015/089354(PCT/US2014/069902), WO 2015/089364 (PCT/US2014/069925), WO 2015/089427(PCT/US2014/070068), WO 2015/089462 (PCT/US2014/070127), WO 2015/089419(PCT/US2014/070057), WO 2015/089465 (PCT/US2014/070135), WO 2015/089486(PCT/US2014/070175), WO2015/058052 (PCT/US2014/061077), WO2015070083(PCT/US2014/064663), WO2015/089354 (PCT/US2014/069902), WO2015/089351(PCT/US2014/069897), WO2015/089364 (PCT/US2014/069925), WO2015/089427(PCT/US2014/070068), WO2015/089473 (PCT/US2014/070152), WO2015/089486(PCT/US2014/070175), WO/2016/04925 (PCT/US2015/051830), WO/2016/094867(PCT/US2015/065385), WO/2016/094872 (PCT/US2015/065393), WO/2016/094874(PCT/US2015/065396), WO/2016/106244 (PCT/US2015/067177)

Reference is further made to Multiplex genome engineering usingCRISPR/Cas systems. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto,R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., &Zhang, F. Science February 15; 339(6121):819-23 (2013); RNA-guidedediting of bacterial genomes using CRISPR-Cas systems. Jiang W., BikardD., Cox D., Zhang F, Marraffini L A. Nat Biotechnol March; 31(3):233-9(2013); One-Step Generation of Mice Carrying Mutations in Multiple Genesby CRISPR/Cas-Mediated Genome Engineering. Wang H., Yang H., Shivalila CS., Dawlaty M M., Cheng A W., Zhang F., Jaenisch R. Cell May 9;153(4):910-8 (2013); Optical control of mammalian endogenoustranscription and epigenetic states. Konermann S, Brigham M D, Trevino AE, Hsu P D, Heidenreich M, Cong L, Platt R J, Scott D A, Church G M,Zhang F. Nature. 2013 Aug. 22; 500(7463):472-6. doi:10.1038/Nature12466. Epub 2013 Aug. 23; Double Nicking by RNA-GuidedCRISPR Cas9 for Enhanced Genome Editing Specificity. Ran, F A., Hsu, PD., Lin, C Y., Gootenberg, J S., Konermann, S., Trevino, A E., Scott, DA., Inoue, A., Matoba, S., Zhang, Y., & Zhang, F. Cell August 28. pii:S0092-8674(13)01015-5. (2013); DNA targeting specificity of RNA-guidedCas9 nucleases. Hsu, P., Scott, D., Weinstein, J., Ran, F A., Konermann,S., Agarwala, V., L i, Y., Fine, E., Wu, X., Shalem, O., Cradick, T J.,Marraffini, L A., Bao, G., & Zhang, F. Nat Biotechnoldoi:10.1038/nbt.2647 (2013); Genome engineering using the CRISPR-Cas9system. Ran, F A., Hsu, P D., Wright, J., Agarwala, V., Scott, D A.,Zhang, F. Nature Protocols November; 8(11):2281-308. (2013);Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells. Shalem, O.,Sanjana, N E., Hartenian, E., Shi, X., Scott, D A., Mikkelson, T.,Heckl, D., Ebert, B L., Root, D E., Doench, J G., Zhang, F. ScienceDecember 12. (2013). [Epub ahead of print]; Crystal structure of cas9 incomplex with guide RNA and target DNA. Nishimasu, H., Ran, F A., Hsu, PD., Konermann, S., Shehata, S I., Dohmae, N., Ishitani, R., Zhang, F.,Nureki, O. Cell February 27. (2014). 156(5):935-49; Genome-wide bindingof the CRISPR endonuclease Cas9 in mammalian cells. Wu X., Scott D A.,Kriz A J., Chiu A C., Hsu P D., Dadon D B., Cheng A W., Trevino A E.,Konermann S., Chen S., Jaenisch R., Zhang F., Sharp P A. Nat Biotechnol.(2014) April 20. doi: 10.1038/nbt.2889; CRISPR-Cas9 Knockin Mice forGenome Editing and Cancer Modeling, Platt et al., Cell 159(2): 440-455(2014) DOI: 10.1016/j.cell.2014.09.014; Development and Applications ofCRISPR-Cas9 for Genome Engineering, Hsu et al, Cell 157, 1262-1278 (Jun.5, 2014) (Hsu 2014); Genetic screens in human cells using theCRISPR/Cas9 system, Wang et al., Science. 2014 Jan. 3; 343(6166): 80-84.doi:10.1126/science.1246981; Rational design of highly active sgRNAs forCRISPR-Cas9-mediated gene inactivation, Doench et al., NatureBiotechnology 32(12):1262-7 (2014) published online 3 Sep. 2014;doi:10.1038/nbt.3026, and In vivo interrogation of gene function in themammalian brain using CRISPR-Cas9, Swiech et al, Nature Biotechnology33, 102-106 (2015) published online 19 Oct. 2014; doi:10.1038/nbt.3055,Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System,Zetsche et al., Cell 163, 1-13 (2015); Discovery and FunctionalCharacterization of Diverse Class 2 CRISPR-Cas Systems, Shmakov et al.,Mol Cell 60(3): 385-397 (2015); Each of these publications, patents,patent publications, and applications, and all documents cited thereinor during their prosecution (“appin cited documents”) and all documentscited or referenced in the appin cited documents, together with anyinstructions, descriptions, product specifications, and product sheetsfor any products mentioned therein or in any document therein andincorporated by reference herein, are hereby incorporated herein byreference, and may be employed in the practice of the invention. Alldocuments (e.g., these patents, patent publications and applications andthe appin cited documents) are incorporated herein by reference to thesame extent as if each individual document was specifically andindividually indicated to be incorporated by reference.

Preferred DNA binding proteins are CRISPR/Cas enzymes or variantsthereof. In certain embodiments, the CRISPR/Cas protein is a class 2CRISPR/Cas protein. In certain embodiments, said CRISPR/Cas protein is atype II, type V, or type VI CRISPR/Cas protein. The CRISPR/Cas systemdoes not require the generation of customized proteins to targetspecific sequences but rather a single Cas protein can be programmed byan RNA guide (gRNA) to recognize a specific nucleic acid target, inother words the Cas enzyme protein can be recruited to a specificnucleic acid target locus (which may comprise or consist of RNA and/orDNA) of interest using said short RNA guide.

In general, the CRISPR/Cas or CRISPR system is as used herein foregoingdocuments refers collectively to elements involved in the expression ofor directing the activity of CRISPR-associated (“Cas”) proteins orgenes, including sequences encoding a Cas protein and a guide RNA. Inthis context of the guide RNA this may include one or more of, a tracr(trans-activating CRISPR) sequence (e.g. tracrRNA or an active partialtracrRNA), a tracr-mate sequence (encompassing a “direct repeat” and atracrRNA-processed partial direct repeat in the context of an endogenousCRISPR system), a guide sequence (also referred to as a “spacer” in thecontext of an endogenous CRISPR system), In general, a CRISPR system ischaracterized by elements that promote the formation of a CRISPR complexat the site of a target sequence. In the context of formation of aCRISPR complex, “target sequence” refers to a sequence to which a guidesequence is designed to have complementarity, where hybridizationbetween a target DNA sequence and a guide sequence promotes theformation of a CRISPR complex.

In certain embodiments, the gRNA comprises a guide sequence fused to atracr mate sequence (or direct repeat), and a tracr sequence Inparticular embodiments, the guide sequence fused to the tracr mate andthe tracr sequence are provided or expressed as discrete RNA sequences.In preferred embodiments, the gRNA is a chimeric guide RNA or singleguide RNA (sgRNA), comprising a guide sequence fused to the tracr matewhich is itself linked to the tracr sequence. In particular embodiments,the CRISPR/Cas system or complex as described herein does not compriseand/or does not rely on the presence of a tracr sequence (e.g. if theCas protein is Cpf1).

As used herein, the term “guide sequence” in the context of a CRISPR/Cassystem, comprises any polynucleotide sequence having sufficientcomplementarity with a target nucleic acid sequence to hybridize withthe target nucleic acid sequence and direct sequence-specific binding ofa nucleic acid-targeting complex to the target nucleic acid sequence. Insome embodiments, the degree of complementarity, when optimally alignedusing a suitable alignment algorithm, is about or more than about 50%,60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment maybe determined with the use of any suitable algorithm for aligningsequences, non-limiting example of which include the Smith-Watermanalgorithm, the Needleman-Wunsch algorithm, algorithms based on theBurrows-Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW,Clustal X, BLAT, Novoalign (Novocraft Technologies; available atwww.novocraft.com), ELAND (Illumina, San Diego, Calif.), SOAP (availableat soap.genomics.org.cn), and Maq (available at maq.sourceforge.net).The ability of a guide sequence (within a nucleic acid-targeting guideRNA) to direct sequence-specific binding of a nucleic acid-targetingcomplex to a target nucleic acid sequence may be assessed by anysuitable assay.

A guide sequence, and hence a nucleic acid-targeting guide RNA may beselected to target any target nucleic acid sequence. The target sequencemay be DNA. The target sequence may be genomic DNA. The target sequencemay be mitochondrial DNA.

In certain embodiments, the gRNA comprises a stem loop, preferably asingle stem loop. In certain embodiments, the direct repeat sequenceforms a stem loop, preferably a single stem loop. In certainembodiments, the spacer length of the guide RNA is from 15 to 35 nt. Incertain embodiments, the spacer length of the guide RNA is at least 15nucleotides. In certain embodiments, the spacer length is from 15 to 17nt, e.g., 15, 16, or 17 nt, from 17 to 20 nt, e.g., 17, 18, 19, or 20nt, from 20 to 24 nt, e.g., 20, 21, 22, 23, or 24 nt, from 23 to 25 nt,e.g., 23, 24, or 25 nt, from 24 to 27 nt, e.g., 24, 25, 26, or 27 nt,from 27-30 nt, e.g., 27, 28, 29, or 30 nt, from 30-35 nt, e.g., 30, 31,32, 33, 34, or 35 nt, or 35 nt or longer. In particular embodiments, theCRISPR/Cas system requires a tracrRNA. The “tracrRNA” sequence oranalogous terms includes any polynucleotide sequence that has sufficientcomplementarity with a crRNA sequence to hybridize. In some embodiments,the degree of complementarity between the tracrRNA sequence and crRNAsequence along the length of the shorter of the two when optimallyaligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%,90%, 95%, 97.5%, 99%, or higher. In some embodiments, the tracr sequenceis about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length. In someembodiments, the tracr sequence and gRNA sequence are contained within asingle transcript, such that hybridization between the two produces atranscript having a secondary structure, such as a hairpin. In anembodiment of the invention, the transcript or transcribedpolynucleotide sequence has at least two or more hairpins. In preferredembodiments, the transcript has two, three, four or five hairpins. In afurther embodiment of the invention, the transcript has at most fivehairpins. In a hairpin structure the portion of the sequence 5′ of thefinal “N” and upstream of the loop may correspond to the tracr matesequence, and the portion of the sequence 3′ of the loop thencorresponds to the tracr sequence. In a hairpin structure the portion ofthe sequence 5′ of the final “N” and upstream of the loop mayalternatively correspond to the tracr sequence, and the portion of thesequence 3′ of the loop corresponds to the tracr mate sequence. Inalternative embodiments, the CRISPR/Cas system does not require atracrRNA, as is known by the skilled person.

In certain embodiments, the guide RNA (capable of guiding Cas to atarget locus) may comprise (1) a guide sequence capable of hybridizingto a target locus and (2) a tracr mate or direct repeat sequence (in 5′to 3′ orientation, or alternatively in 3′ to 5′ orientation, dependingon the type of Cas protein, as is known by the skilled person). Inparticular embodiments, the CRISPR/Cas protein is characterized in thatit makes use of a guide RNA comprising a guide sequence capable ofhybridizing to a target locus and a direct repeat sequence, and does notrequire a tracrRNA. In particular embodiments, where the CRISPR/Casprotein is characterized in that it makes use of a tracrRNA, the guidesequence, tracr mate, and tracr sequence may reside in a single RNA,i.e. an sgRNA (arranged in a 5′ to 3′ orientation or alternativelyarranged in a 3′ to 5′ orientation), or the tracr RNA may be a differentRNA than the RNA containing the guide and tracr mate sequence. In theseembodiments, the tracr hybridizes to the tracr mate sequence and directsthe CRISPR/Cas complex to the target sequence.

In particular embodiments, the DNA binding protein is a catalyticallyactive protein. In these embodiments, the formation of a nucleicacid-targeting complex (comprising a guide RNA hybridized to a targetsequence results in modification (such as cleavage) of one or both DNAor RNA strands in or near (e.g., within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,20, 50, or more base pairs from) the target sequence. As used herein theterm “sequence(s) associated with a target locus of interest” refers tosequences near the vicinity of the target sequence (e.g. within 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from the targetsequence, wherein the target sequence is comprised within a target locusof interest). The skilled person will be aware of specific cut sites forselected CRISPR/Cas systems, relative to the target sequence, which asis known in the art may be within the target sequence or alternatively3′ or 5′ of the target sequence.

Accordingly, in particular embodiments, the DNA binding protein hasnucleic acid cleavage activity. In some embodiments, the nuclease asdescribed herein may direct cleavage of one or both nucleic acid (DNA,RNA, or hybrids, which may be single or double stranded) strands at thelocation of or near a target sequence, such as within the targetsequence and/or within the complement of the target sequence or atsequences associated with the target sequence. In some embodiments, thenucleic acid-targeting effector protein may direct cleavage of one orboth DNA or RNA strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 50, 100, 200, 500, or more base pairs from the first or lastnucleotide of a target sequence. In some embodiments, the cleavage maybe blunt (e.g. for Cas9, such as SaCas9 or SpCas9). In some embodiments,the cleavage may be staggered (e.g. for Cpf1), i.e. generating stickyends. In some embodiments, the cleavage is a staggered cut with a 5′overhang. In some embodiments, the cleavage is a staggered cut with a 5′overhang of 1 to 5 nucleotides, preferably of 4 or 5 nucleotides. Insome embodiments, the cleavage site is upstream of the PAM. In someembodiments, the cleavage site is downstream of the PAM.

In certain embodiments, the target sequence should be associated with aPAM (protospacer adjacent motif) or PFS (protospacer flanking sequenceor site); that is, a short sequence recognized by the CRISPR complex.The precise sequence and length requirements for the PAM differdepending on the CRISPR enzyme used, but PAMs are typically 2-5 basepair sequences adjacent the protospacer (that is, the target sequence).Examples of PAM sequences are given in the examples section below, andthe skilled person will be able to identify further PAM sequences foruse with a given CRISPR enzyme. Further, engineering of the PAMInteracting (PI) domain may allow programing of PAM specificity, improvetarget site recognition fidelity, and increase the versatility of theCas, e.g. Cas9, genome engineering platform. Cas proteins, such as Cas9proteins may be engineered to alter their PAM specificity, for exampleas described in Kleinstiver B P et al. Engineered CRISPR-Cas9 nucleaseswith altered PAM specificities. Nature. 2015 Jul. 23; 523(7561):481-5.doi: 10.1038/nature14592. In some embodiments, the method comprisesallowing a CRISPR complex to bind to the target polynucleotide to effectcleavage of said target polynucleotide thereby modifying the targetpolynucleotide, wherein the CRISPR complex comprises a CRISPR enzymecomplexed with a guide sequence hybridized to a target sequence withinsaid target polynucleotide, wherein said guide sequence is linked to atracr mate sequence which in turn hybridizes to a tracr sequence. Theskilled person will understand that other Cas proteins may be modifiedanalogously.

In some embodiments, the nucleic acid-targeting effector protein may bemutated with respect to a corresponding wild-type enzyme such that themutated nucleic acid-targeting effector protein lacks the ability tocleave one or both DNA strands of a target polynucleotide containing atarget sequence. As a further example, two or more catalytic domains ofa Cas protein (e.g. RuvC I, RuvC II, and RuvC III or the HNH domain of aCas9 protein) may be mutated to produce a mutated Cas protein whichcleaves only one DNA strand of a target sequence.

In particular embodiments, the nucleic acid-targeting effector proteinmay be mutated with respect to a corresponding wild-type enzyme suchthat the mutated nucleic acid-targeting effector protein lackssubstantially all DNA cleavage activity. In some embodiments, a nucleicacid-targeting effector protein may be considered to substantially lackall DNA and/or RNA cleavage activity when the cleavage activity of themutated enzyme is about no more than 25%, 10%, 5%, 1%, 0.1%, 0.01%, orless of the nucleic acid cleavage activity of the non-mutated form ofthe enzyme; an example can be when the nucleic acid cleavage activity ofthe mutated form is nil or negligible as compared with the non-mutatedform.

As used herein, the term “modified” Cas generally refers to a Casprotein having one or more modifications or mutations (including pointmutations, truncations, insertions, deletions, chimeras, fusionproteins, etc.) compared to the wild type Cas protein from which it isderived. By derived is meant that the derived enzyme is largely based,in the sense of having a high degree of sequence homology with, awildtype enzyme, but that it has been mutated (modified) in some way asknown in the art or as described herein.

As detailed above, in certain embodiments, the nuclease as referred toherein is modified. As used herein, the term “modified” refers to whichmay or may not have an altered functionality. By means of example, andin particular with reference to Cas proteins, modifications which do notresult in an altered functionality include for instance codonoptimization for expression into a particular host, or providing thenuclease with a particular marker (e.g. for visualization).Modifications with may result in altered functionality may also includemutations, including point mutations, insertions, deletions, truncations(including split nucleases), etc., as well as chimeric nucleases (e.g.comprising domains from different orthologues or homologues) or fusionproteins. Fusion proteins may without limitation include for instancefusions with heterologous domains or functional domains (e.g.localization signals, catalytic domains, etc.). Accordingly, in certainembodiments, the modified nuclease may be used as a generic nucleic acidbinding protein with fusion to or being operably linked to a functionaldomain. In certain embodiments, various different modifications may becombined (e.g. a mutated nuclease which is catalytically inactive andwhich further is fused to a functional domain, such as for instance toinduce DNA methylation or another nucleic acid modification, such asincluding without limitation a break (e.g. by a different nuclease(domain)), a mutation, a deletion, an insertion, a replacement, aligation, a digestion, a break or a recombination). As used herein,“altered functionality” includes without limitation an alteredspecificity (e.g. altered target recognition, increased (e.g. “enhanced”Cas proteins) or decreased specificity, or altered PAM recognition),altered activity (e.g. increased or decreased catalytic activity,including catalytically inactive nucleases or nickases), and/or alteredstability (e.g. fusions with destalilization domains). Suitableheterologous domains include without limitation a nuclease, a ligase, arepair protein, a methyltransferase, (viral) integrase, a recombinase, atransposase, an argonaute, a cytidine deaminase, a retron, a group IIintron, a phosphatase, a phosphorylase, a sulpfurylase, a kinase, apolymerase, an exonuclease, etc. Examples of all these modifications areknown in the art. It will be understood that a “modified” nuclease asreferred to herein, and in particular a “modified” Cas or “modified”CRISPR/Cas system or complex preferably still has the capacity tointeract with or bind to the polynucleic acid (e.g. in complex with thegRNA).

By means of further guidance and without limitation, in certainembodiments, the nuclease may be modified as detailed below. As alreadyindicated, more than one of the indicated modifications may be combined.For instance, codon optimization may be combined with NLS or NESfusions, catalytically inactive nuclease modifications or nickasemutants may be combined with fusions to functional (heterologous)domains, etc.

In certain embodiments, the nuclease, and in particular the Cas proteinsof prokaryotic origin, may be codon optimized for expression into aparticular host (cell). An example of a codon optimized sequence, is inthis instance a sequence optimized for expression in a eukaryote, e.g.,humans (i.e. being optimized for expression in humans), or for anothereukaryote, animal or mammal as herein discussed; see, e.g., SaCas9 humancodon optimized sequence in WO 2014/093622 (PCT/US2013/074667). Whilstthis is preferred, it will be appreciated that other examples arepossible and codon optimization for a host species other than human, orfor codon optimization for specific organs is known. In someembodiments, an enzyme coding sequence encoding a Cas is codon optimizedfor expression in particular cells, such as eukaryotic cells. Theeukaryotic cells may be those of or derived from a particular organism,such as a mammal, including but not limited to human, or non-humaneukaryote or animal or mammal as herein discussed, e.g., mouse, rat,rabbit, dog, livestock, or non-human mammal or primate. In someembodiments, processes for modifying the germ line genetic identity ofhuman beings and/or processes for modifying the genetic identity ofanimals which are likely to cause them suffering without any substantialmedical benefit to man or animal, and also animals resulting from suchprocesses, may be excluded. In general, codon optimization refers to aprocess of modifying a nucleic acid sequence for enhanced expression inthe host cells of interest by replacing at least one codon (e.g. aboutor more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) ofthe native sequence with codons that are more frequently or mostfrequently used in the genes of that host cell while maintaining thenative amino acid sequence. Various species exhibit particular bias forcertain codons of a particular amino acid. Codon bias (differences incodon usage between organisms) often correlates with the efficiency oftranslation of messenger RNA (mRNA), which is in turn believed to bedependent on, among other things, the properties of the codons beingtranslated and the availability of particular transfer RNA (tRNA)molecules. The predominance of selected tRNAs in a cell is generally areflection of the codons used most frequently in peptide synthesis.Accordingly, genes can be tailored for optimal gene expression in agiven organism based on codon optimization. Codon usage tables arereadily available, for example, at the “Codon Usage Database” availableat www.kazusa.orjp/codon/ and these tables can be adapted in a number ofways. See Nakamura, Y., et al. “Codon usage tabulated from theinternational DNA sequence databases: status for the year 2000” Nucl.Acids Res. 28:292 (2000). Computer algorithms for codon optimizing aparticular sequence for expression in a particular host cell are alsoavailable, such as Gene Forge (Aptagen; Jacobus, Pa.), are alsoavailable. In some embodiments, one or more codons (e.g. 1, 2, 3, 4, 5,10, 15, 20, 25, 50, or more, or all codons) in a sequence encoding a Cascorrespond to the most frequently used codon for a particular aminoacid. Codon optimization may be for expression into any desired host(cell), including mammalian, plant, algae, or yeast.

In certain embodiments, the nuclease, in particular the Cas protein, maycomprise one or more modifications resulting in enhanced activity and/orspecificity, such as including mutating residues that stabilize thetargeted or non-targeted strand (e.g. eCas9; “Rationally engineered Cas9nucleases with improved specificity”, Slaymaker et al. (2016), Science,351(6268):84-88, incorporated herewith in its entirety by reference). Incertain embodiments, the altered or modified activity of the engineeredCRISPR protein comprises increased targeting efficiency or decreasedoff-target binding. In certain embodiments, the altered activity of theengineered CRISPR protein comprises modified cleavage activity. Incertain embodiments, the altered activity comprises increased cleavageactivity as to the target polynucleotide loci. In certain embodiments,the altered activity comprises decreased cleavage activity as to thetarget polynucleotide loci. In certain embodiments, the altered activitycomprises decreased cleavage activity as to off-target polynucleotideloci. In certain embodiments, the altered or modified activity of themodified nuclease comprises altered helicase kinetics. In certainembodiments, the modified nuclease comprises a modification that altersassociation of the protein with the nucleic acid molecule comprising RNA(in the case of a Cas protein), or a strand of the target polynucleotideloci, or a strand of off-target polynucleotide loci. In an aspect of theinvention, the engineered CRISPR protein comprises a modification thatalters formation of the CRISPR complex. In certain embodiments, thealtered activity comprises increased cleavage activity as to off-targetpolynucleotide loci. Accordingly, in certain embodiments, there isincreased specificity for target polynucleotide loci as compared tooff-target polynucleotide loci. In other embodiments, there is reducedspecificity for target polynucleotide loci as compared to off-targetpolynucleotide loci. In certain embodiments, the mutations result indecreased off-target effects (e.g. cleavage or binding properties,activity, or kinetics), such as in case for Cas proteins for instanceresulting in a lower tolerance for mismatches between target and gRNA.Other mutations may lead to increased off-target effects (e.g. cleavageor binding properties, activity, or kinetics). Other mutations may leadto increased or decreased on-target effects (e.g. cleavage or bindingproperties, activity, or kinetics). In certain embodiments, themutations result in altered (e.g. increased or decreased) helicaseactivity, association or formation of the functional nuclease complex(e.g. CRISPR/Cas complex). In certain embodiments, the mutations resultin an altered PAM recognition, i.e. a different PAM may be (in additionor in the alternative) be recognized, compared to the unmodified Casprotein (see e.g. “Engineered CRISPR-Cas9 nucleases with altered PAMspecificities”, Kleinstiver et al. (2015), Nature, 523(7561):481-485,incorporated herein by reference in its entirety). Particularlypreferred mutations include positively charged residues and/or(evolutionary) conserved residues, such as conserved positively chargedresidues, in order to enhance specificity. In certain embodiments, suchresidues may be mutated to uncharged residues, such as alanine.

In certain embodiments, the nuclease, in particular the Cas protein, maycomprise one or more modifications resulting in a nuclease that hasreduced or no catalytic activity, or alternatively (in case of nucleasesthat target double stranded nucleic acids) resulting in a nuclease thatonly cleaves one strand, i.e. a nickase. By means of further guidance,and without limitation, for example, an aspartate-to-alaninesubstitution (D10A) in the RuvC I catalytic domain of Cas9 from S.pyogenes converts Cas9 from a nuclease that cleaves both strands to anickase (cleaves a single strand). Other examples of mutations thatrender Cas9 a nickase include, without limitation, H840A, N854A, andN863A. As further guidance, where the enzyme is not SpCas9, mutationsmay be made at any or all residues corresponding to positions 10, 762,840, 854, 863 and/or 986 of SpCas9 (which may be ascertained forinstance by standard sequence comparison tools). In particular, any orall of the following mutations are preferred in SpCas9: D10A, E762A,H840A, N854A, N863A and/or D986A; as well as conservative substitutionfor any of the replacement amino acids is also envisaged. As a furtherexample, two or more catalytic domains of Cas9 (RuvC I, RuvC II, andRuvC III or the HNH domain) may be mutated to produce a mutated Cas9substantially lacking all DNA cleavage activity. In some embodiments, aD10A mutation is combined with one or more of H840A, N854A, or N863Amutations to produce a Cas9 enzyme substantially lacking all DNAcleavage activity. In some embodiments, a Cas is considered tosubstantially lack all DNA cleavage activity when the DNA cleavageactivity of the mutated enzyme is about no more than 25%, 10%, 5%, 1%,0.1%, 0.01%, or less of the DNA cleavage activity of the non-mutatedform of the enzyme; an example can be when the DNA cleavage activity ofthe mutated form is nil or negligible as compared with the non-mutatedform. Thus, the Cas may comprise one or more mutations and may be usedas a generic DNA binding protein with or without fusion to a functionaldomain. The mutations may be artificially introduced mutations or gain-or loss-of-function mutations. The mutations may include but are notlimited to mutations in one of the catalytic domains (e.g., D10 andH840) in the RuvC and HNH catalytic domains respectively; or the CRISPRenzyme can comprise one or more mutations selected from the groupconsisting of D10A, E762A, H840A, N854A, N863A or D986A and/or one ormore mutations in a RuvC1 or HNH domain of the Cas or has a mutation asotherwise as discussed herein.

In certain embodiments, the nuclease is a split nuclease (see e.g. “Asplit-Cas9 architecture for inducible genome editing and transcriptionmodulation”, Zetsche et al. (2015), Nat Biotechnol. 33(2):139-42,incorporated herein by reference in its entirety). In a split nuclease,the activity (which may be a modified activity, as described hereinelsewhere), relies on the two halves of the split nuclease to be joined,i.e. each half of the split nuclease does not possess the requiredactivity, until joined. As further guidance, and without limitation,with specific reference to Cas9, a split Cas9 may result from splittingthe Cas9 at any one of the following split points, according or withreference to SpCas9: a split position between 202A/203S; a splitposition between 255F/256D; a split position between 310E/3111; a splitposition between 534R/535K; a split position between 572E/573C; a splitposition between 713S/714G; a split position between 1003L/104E; a splitposition between 1054G/1055E; a split position between 1114N/1115S; asplit position between 1152K/1153S; a split position between1245K/1246G; or a split between 1098 and 1099. Identifying potentialsplit sides is most simply done with the help of a crystal structure.For Sp mutants, it should be readily apparent what the correspondingposition for, for example, a sequence alignment. For non-Sp enzymes onecan use the crystal structure of an ortholog if a relatively high degreeof homology exists between the ortholog and the intended Cas9. Ideally,the split position should be located within a region or loop.Preferably, the split position occurs where an interruption of the aminoacid sequence does not result in the partial or full destruction of astructural feature (e.g. alpha-helixes or beta-sheets). Unstructuredregions (regions that did not show up in the crystal structure becausethese regions are not structured enough to be “frozen” in a crystal) areoften preferred options. In certain embodiments, a functional domain maybe provided on each of the split halves, thereby allowing the formationof homodimers or heterodimers. The functional domains may be (inducible)interact, thereby joining the split halves, and reconstituting(modified) nuclease activity. By means of example, an inducer energysource may inducibly allow dimerization of the split halves, throughappropriate fusion partners. An inducer energy source may be consideredto be simply an inducer or a dimerizing agent. The term ‘inducer energysource’ is used herein throughout for consistency. The inducer energysource (or inducer) acts to reconstitute the Cas9. In some embodiments,the inducer energy source brings the two parts of the Cas9 togetherthrough the action of the two halves of the inducible dimer. The twohalves of the inducible dimer therefore are brought tougher in thepresence of the inducer energy source. The two halves of the dimer willnot form into the dimer (dimerize) without the inducer energy source.Thus, the two halves of the inducible dimer cooperate with the inducerenergy source to dimerize the dimer. This in turn reconstitutes the Cas9by bringing the first and second parts of the Cas9 together. The CRISPRenzyme fusion constructs each comprise one part of the split Cas9. Theseare fused, preferably via a linker such as a GlySer linker describedherein, to one of the two halves of the dimer. The two halves of thedimer may be substantially the same two monomers that together that formthe homodimer, or they may be different monomers that together form theheterodimer. As such, the two monomers can be thought of as one half ofthe full dimer. The Cas9 is split in the sense that the two parts of theCas9 enzyme substantially comprise a functioning Cas9. That Cas9 mayfunction as a genome editing enzyme (when forming a complex with thetarget DNA and the guide), such as a nickase or a nuclease (cleavingboth strands of the DNA), or it may be a deadCas9 which is essentially aDNA-binding protein with very little or no catalytic activity, due totypically two or more mutations in its catalytic domains as describedherein further.

In certain embodiments, the nuclease may comprise one or more additional(heterologous) functional domains, i.e. the modified nuclease is afusion protein comprising the nuclease itself and one or more additionaldomains, which may be fused C-terminally or N-terminally to thenuclease, or alternatively inserted at suitable and appropriate sitedinternally within the nuclease (preferably without perturbing itsfunction, which may be an otherwise modified function, such as includingreduced or absent catalytic activity, nickase activity, etc.). any typeof functional domain may suitably be used, such as without limitationincluding functional domains having one or more of the followingactivities: (DNA or RNA) methyltransferase activity, methylase activity,demethylase activity, DNA hydroxylmethylase domain, histone acetylasedomain, histone deacetylases domain, transcription or translationactivation activity, transcription or translation repression activity,transcription or translation release factor activity, histonemodification activity, nuclease activity, single-strand RNA cleavageactivity, double-strand RNA cleavage activity, single-strand DNAcleavage activity, double-strand DNA cleavage activity, nucleic acidbinding activity, a protein acetyltransferase, a protein deacetylase, aprotein methyltransferase, a protein deaminase, a protein kinase, aprotein phosphatase, transposase domain, integrase domain, recombinasedomain, resolvase domain, invertase domain, protease domain, repressordomain, activator domain, nuclear-localization signal domains,transcription-regulatory protein (or transcription complex recruiting)domain, cellular uptake activity associated domain, nucleic acid bindingdomain, antibody presentation domain, histone modifying enzymes,recruiter of histone modifying enzymes; inhibitor of histone modifyingenzymes, histone methyltransferase, histone demethylase, histone kinase,histone phosphatase, histone ribosylase, histone deribosylase, histoneubiquitinase, histone deubiquitinase, histone biotinase, histone tailprotease, HDACs, histone methyltransferases (HMTs), and histoneacetyltransferase (HAT) inhibitors, as well as HDAC and HMT recruitingproteins, HDAC Effector Domains, HDAC Recruiter Effector Domains,Histone Methyltransferase (HMT) Effector Domains, HistoneMethyltransferase (HMT) Recruiter Effector Domains, or HistoneAcetyltransferase Inhibitor Effector Domains. In some embodiments, thefunctional domain is an epigenetic regulator; see, e.g., Zhang et al.,U.S. Pat. No. 8,507,272 (incorporated herein by reference in itsentirety). In some embodiments, the functional domain is atranscriptional activation domain, such as VP64, p65, MyoD1, HSF1, RTA,SETT/9 or a histone acetyltransferase. In some embodiments, thefunctional domain is a transcription repression domain, such as KRAB. Insome embodiments, the transcription repression domain is SID, orconcatemers of SID (eg SID4X), NuE, or NcoR. In some embodiments, thefunctional domain is an epigenetic modifying domain, such that anepigenetic modifying enzyme is provided. In some embodiments, thefunctional domain is an activation domain, which may be the P65activation domain. In some embodiments, the functional domain comprisesnuclease activity. In one such embodiment, the functional domain maycomprise Fokl. Mention is made of U.S. Pat. Pub. 2014/0356959, U.S. Pat.Pub. 2014/0342456, U.S. Pat. Pub. 2015/0031132, and Mali, P. et al.,2013, Science 339(6121):823-6, doi: 10.1126/science.1232033, publishedonline 3 Jan. 2013 and through the teachings herein the inventioncomprehends methods and materials of these documents applied inconjunction with the teachings herein. It is to be understood that alsodestabilization domains or localization domains as described hereinelsewhere are encompassed by the generic term “functional domain”. Incertain embodiments, one or more functional domains are associated withthe nuclease itself. In some embodiments, one or more functional domainsare associated with an adaptor protein, for example as used with themodified guides of Konnerman et al. (Nature 517(7536): 583-588, 2015;incorporated herein by reference in its entirety), and hene form part ofa Synergistic activator mediator (SAM) complex. The adaptor proteins mayinclude but are not limited to orthogonal RNA-binding protein/aptamercombinations that exist within the diversity of bacteriophage coatproteins. A list of such coat proteins includes, but is not limited to:Qβ, F2, GA, fr, JP501, M12, R17, BZ13, JP34, JP500, KU1, M11, MX1, TW18,VK, SP, FI, ID2, NL95, TW19, AP205, ϕCb5, ϕCb8r, ϕCb12r, ϕCb23r, 7s andPRR1. These adaptor proteins or orthogonal RNA binding proteins canfurther recruit effector proteins or fusions which comprise one or morefunctional domains.

In certain embodiments, the nuclease, in particular the Cas protein, maycomprise one or more modifications resulting in a destabilized nucleasewhen expressed in a host (cell). Such may be achieved by fusion of thenuclease with a destabilization domain (DD). Destabilizing domains havegeneral utility to confer instability to a wide range of proteins; see,e.g., Miyazaki, J Am Chem Soc. Mar. 7, 2012; 134(9): 3942-3945,incorporated herein by reference. CMP8 or 4-hydroxytamoxifen can bedestabilizing domains. More generally, A temperature-sensitive mutant ofmammalian DHFR (DHFRts), a destabilizing residue by the N-end rule, wasfound to be stable at a permissive temperature but unstable at 37° C.The addition of methotrexate, a high-affinity ligand for mammalian DHFR,to cells expressing DHFRts inhibited degradation of the proteinpartially. This was an important demonstration that a small moleculeligand can stabilize a protein otherwise targeted for degradation incells. A rapamycin derivative was used to stabilize an unstable mutantof the FRB domain of mTOR (FRB*) and restore the function of the fusedkinase, GSK-3β.6,7 This system demonstrated that ligand-dependentstability represented an attractive strategy to regulate the function ofa specific protein in a complex biological environment. A system tocontrol protein activity can involve the DD becoming functional when theubiquitin complementation occurs by rapamycin induced dimerization ofFK506-binding protein and FKBP12. Mutants of human FKBP12 or ecDHFRprotein can be engineered to be metabolically unstable in the absence oftheir high-affinity ligands, Shield-1 or trimethoprim (TMP),respectively. These mutants are some of the possible destabilizingdomains (DDs) useful in the practice of the invention and instability ofa DD as a fusion with a CRISPR enzyme confers to the CRISPR proteindegradation of the entire fusion protein by the proteasome. Shield-1 andTMP bind to and stabilize the DD in a dose-dependent manner. Theestrogen receptor ligand binding domain (ERLBD, residues 305-549 ofERS1) can also be engineered as a destabilizing domain. Since theestrogen receptor signaling pathway is involved in a variety of diseasessuch as breast cancer, the pathway has been widely studied and numerousagonist and antagonists of estrogen receptor have been developed. Thus,compatible pairs of ERLBD and drugs are known. There are ligands thatbind to mutant but not wild-type forms of the ERLBD. By using one ofthese mutant domains encoding three mutations (L384M, M421G, G521R)12,it is possible to regulate the stability of an ERLBD-derived DD using aligand that does not perturb endogenous estrogen-sensitive networks. Anadditional mutation (Y537S) can be introduced to further destabilize theERLBD and to configure it as a potential DD candidate. This tetra-mutantis an advantageous DD development. The mutant ERLBD can be fused to aCRISPR enzyme and its stability can be regulated or perturbed using aligand, whereby the CRISPR enzyme has a DD. Another DD can be a 12-kDa(107-amino-acid) tag based on a mutated FKBP protein, stabilized byShield1 ligand; see, e.g., Nature Methods 5, (2008). For instance a DDcan be a modified FK506 binding protein 12 (FKBP12) that binds to and isreversibly stabilized by a synthetic, biologically inert small molecule,Shield-1; see, e.g., Banaszynski L A, Chen L C, Maynard-Smith L A, Ooi AG, Wandless T J. A rapid, reversible, and tunable method to regulateprotein function in living cells using synthetic small molecules. Cell.2006; 126:995-1004; Banaszynski L A, Sellmyer M A, Contag C H, WandlessT J, Thorne S H. Chemical control of protein stability and function inliving mice. Nat Med. 2008; 14:1123-1127; Maynard-Smith L A, Chen L C,Banaszynski L A, Ooi A G, Wandless T J. A directed approach forengineering conditional protein stability using biologically silentsmall molecules. The Journal of biological chemistry. 2007;282:24866-24872; and Rodriguez, Chem Biol. Mar. 23, 2012; 19(3):391-398—all of which are incorporated herein by reference and may beemployed in the practice of the invention in selected a DD to associatewith a CRISPR enzyme in the practice of this invention. As can be seen,the knowledge in the art includes a number of DDs, and the DD can beassociated with, e.g., fused to, advantageously with a linker, to aCRISPR enzyme, whereby the DD can be stabilized in the presence of aligand and when there is the absence thereof the DD can becomedestabilized, whereby the CRISPR enzyme is entirely destabilized, or theDD can be stabilized in the absence of a ligand and when the ligand ispresent the DD can become destabilized; the DD allows the CRISPR enzymeand hence the CRISPR-Cas complex or system to be regulated orcontrolled—turned on or off so to speak, to thereby provide means forregulation or control of the system, e.g., in an in vivo or in vitroenvironment. For instance, when a protein of interest is expressed as afusion with the DD tag, it is destabilized and rapidly degraded in thecell, e.g., by proteasomes. Thus, absence of stabilizing ligand leads toa D associated Cas being degraded. When a new DD is fused to a proteinof interest, its instability is conferred to the protein of interest,resulting in the rapid degradation of the entire fusion protein. Peakactivity for Cas is sometimes beneficial to reduce off-target effects.Thus, short bursts of high activity are preferred. The present inventionis able to provide such peaks. In some senses the system is inducible.In some other senses, the system repressed in the absence of stabilizingligand and de-repressed in the presence of stabilizing ligand. By meansof example, and without limitation, in some embodiments, the DD is ER50.A corresponding stabilizing ligand for this DD is, in some embodiments,4HT. As such, in some embodiments, one of the at least one DDs is ER50and a stabilizing ligand therefor is 4HT or CMP8. In some embodiments,the DD is DHFR50. A corresponding stabilizing ligand for this DD is, insome embodiments, TMP. As such, in some embodiments, one of the at leastone DDs is DHFR50 and a stabilizing ligand therefor is TMP. In someembodiments, the DD is ER50. A corresponding stabilizing ligand for thisDD is, in some embodiments, CMP8. CMP8 may therefore be an alternativestabilizing ligand to 4HT in the ER50 system. While it may be possiblethat CMP8 and 4HT can/should be used in a competitive matter, some celltypes may be more susceptible to one or the other of these two ligands,and from this disclosure and the knowledge in the art the skilled personcan use CMP8 and/or 4HT. More than one (the same or different) DD may bepresent, and may be fused for instance C-terminally, or N-terminally, oreven internally at suitable locations. Having two or more DDs which areheterologous may be advantageous as it would provide a greater level ofdegradation control.

In some embodiments, the fusion protein as described herein may comprisea linker between the nuclease and the fusion partner (e.g. functionaldomain). In some embodiments, the linker is a GlySer linker. Attachmentof a functional domain or fusion protein can be via a linker, e.g., aflexible glycine-serine (GlyGlyGlySer) or (GGGS)3 or a rigidalpha-helical linker such as (Ala(GluAlaAlaAlaLys)Ala). Linkers such as(GGGGS)3 are preferably used herein to separate protein or peptidedomains. (GGGGS)3 is preferable because it is a relatively long linker(15 amino acids). The glycine residues are the most flexible and theserine residues enhance the chance that the linker is on the outside ofthe protein. (GGGGS)6 (GGGGS)9 or (GGGGS)12 may preferably be used asalternatives. Other preferred alternatives are (GGGGS)1, (GGGGS)2,(GGGGS)4, (GGGGS)5, (GGGGS)7, (GGGGS)8, (GGGGS)10, or (GGGGS)11.Alternative linkers are available, but highly flexible linkers arethought to work best to allow for maximum opportunity for the 2 parts ofthe Cas9 to come together and thus reconstitute Cas9 activity. Onealternative is that the NLS of nucleoplasmin can be used as a linker.For example, a linker can also be used between the Cas9 and anyfunctional domain. Again, a (GGGGS)3 linker may be used here (or the 6,9, or 12 repeat versions therefore) or the NLS of nucleoplasmin can beused as a linker between Cas9 and the functional domain.

In some embodiments, the nuclease is fused to one or more localizationsignals, such as nuclear localization sequences (NLSs), such as about ormore than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs. In someembodiments, the nuclease comprises about or more than about 1, 2, 3, 4,5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, about ormore than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or nearthe carboxy-terminus, or a combination of these (e.g. zero or at leastone or more NLS at the amino-terminus and zero or at one or more NLS atthe carboxy terminus). When more than one NLS is present, each may beselected independently of the others, such that a single NLS may bepresent in more than one copy and/or in combination with one or moreother NLSs present in one or more copies. In a preferred embodiment ofthe invention, the nuclease comprises at most 6 NLSs. In someembodiments, an NLS is considered near the N- or C-terminus when thenearest amino acid of the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20,25, 30, 40, 50, or more amino acids along the polypeptide chain from theN- or C-terminus. Non-limiting examples of NLSs include an NLS sequencederived from: the NLS of the SV40 virus large T-antigen, having theamino acid sequence PKKKRKV; the NLS from nucleoplasmin (e.g. thenucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK); thec-myc NLS having the amino acid sequence PAAKRVKLD or RQRRNELKRSP; thehRNPA1 M9 NLS having the sequenceNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY; the sequenceRMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV of the IBB domain fromimportin-alpha; the sequences VSRKRPRP and PPKKARED of the myoma Tprotein; the sequence POPKKKPL of human p53; the sequence SALIKKKKKMAPof mouse c-abl IV; the sequences DRLRR and PKQKKRK of the influenzavirus NS1; the sequence RKLKKKIKKL of the Hepatitis virus delta antigen;the sequence REKKKFLKRR of the mouse Mx1 protein; the sequenceKRKGDEVDGVDEVAKKKSKK of the human poly(ADP-ribose) polymerase; and thesequence RKCLQAGMNLEARKTKK of the steroid hormone receptors (human)glucocorticoid.

With particular reference to the CRISPR/Cas system as described herein,besides the Cas protein, in addition or in the alternative, the gRNAand/or tracr (where applicable) and/or tracr mate (or direct repeat) maybe modified. Suitable modifications include, without limitation deadguides, escorted guides, protected guides, or guides provided withaptamers, suitable for ligating to, binding or recruiting functionaldomains (see e.g. also elsewhere herein the reference to synergisticactivator mediators (SAM)). Mention is also made of WO/2016/049258(FUNCTIONAL SCREENING WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS(SAM)), WO/2016/094867 (PROTECTED GUIDE RNAS (PGRNAS); WO/2016/094872(DEAD GUIDES FOR CRISPR TRANSCRIPTION FACTORS); WO/2016/094874 (ESCORTEDAND FUNCTIONALIZED GUIDES FOR CRISPR-CAS SYSTEMS); all incorporatedherein by reference. In certain embodiments, the tracr sequence (whereappropriate) and/or tracr mate sequence (direct repeat), may compriseone or more protein-interacting RNA aptamers. The one or more aptamersmay be located in the tetraloop and/or stemloop 2 of the tracr sequence.The one or more aptamers may be capable of binding MS2 bacteriophagecoat protein. In certain embodiments, the gRNA (or trace or tracr mate)is modified by truncations, and/or incorporation of one or moremismatches vis-à-vis the intended target sequence or sequence tohybridize with.

By means of further guidance, and without limitation, in certainembodiments, the gRNA is a dead gRNA (dgRNA), which are guide sequenceswhich are modified in a manner which allows for formation of the CRISPRcomplex and successful binding to the target, while at the same time,not allowing for successful nuclease activity (i.e. without nucleaseactivity/without indel activity). These dead guides or dead guidesequences can be thought of as catalytically inactive orconformationally inactive with regard to nuclease activity. Severalstructural parameters allow for a proper framework to arrive at suchdead guides. Dead guide sequences are shorter than respective guidesequences which result in active Cas-specific indel formation. Deadguides are 5%, 10%, 20%, 30%, 40%, 50%, shorter than respective guidesdirected to the same Cas protein leading to active Cas-specific indelformation. Guide RNA comprising a dead guide may be modified to furtherinclude elements in a manner which allow for activation or repression ofgene activity, in particular protein adaptors (e.g. aptamers) asdescribed herein elsewhere allowing for functional placement of geneeffectors (e.g. activators or repressors of gene activity). One exampleis the incorporation of aptamers, as explained herein and in the stateof the art. By engineering the gRNA comprising a dead guide toincorporate protein-interacting aptamers (Konermann et al.,“Genome-scale transcription activation by an engineered CRISPR-Cas9complex,” doi:10.1038/nature14136, incorporated herein by reference),one may assemble a synthetic transcription activation complex consistingof multiple distinct effector domains. Such may be modeled after naturaltranscription activation processes. For example, an aptamer, whichselectively binds an effector (e.g. an activator or repressor; dimerizedMS2 bacteriophage coat proteins as fusion proteins with an activator orrepressor), or a protein which itself binds an effector (e.g. activatoror repressor) may be appended to a dead gRNA tetraloop and/or astem-loop 2. In the case of MS2, the fusion protein MS2-VP64 binds tothe tetraloop and/or stem-loop 2 and in turn mediates transcriptionalup-regulation, for example for Neurog2. Other transcriptional activatorsare, for example, VP64. P65, HSF1, and MyoD1. By mere example of thisconcept, replacement of the MS2 stem-loops with PP7-interactingstem-loops may be used to recruit repressive elements.

By means of further guidance, and without limitation, in certainembodiments, the gRNA is an escorted gRNA (egRNA). By “escorted” ismeant that the CRISPR-Cas system or complex or guide is delivered to aselected time or place within a cell, so that activity of the CRISPR-Cassystem or complex or guide is spatially or temporally controlled. Forexample, the activity and destination of the CRISPR-Cas system orcomplex or guide may be controlled by an escort RNA aptamer sequencethat has binding affinity for an aptamer ligand, such as a cell surfaceprotein or other localized cellular component. Alternatively, the escortaptamer may for example be responsive to an aptamer effector on or inthe cell, such as a transient effector, such as an external energysource that is applied to the cell at a particular time. The escortedCpf1 CRISPR-Cas systems or complexes have a gRNA with a functionalstructure designed to improve gRNA structure, architecture, stability,genetic expression, or any combination thereof. Such a structure caninclude an aptamer. Aptamers are biomolecules that can be designed orselected to bind tightly to other ligands, for example using a techniquecalled systematic evolution of ligands by exponential enrichment (SELEX;Tuerk C, Gold L: “Systematic evolution of ligands by exponentialenrichment: RNA ligands to bacteriophage T4 DNA polymerase.” Science1990, 249:505-510). Nucleic acid aptamers can for example be selectedfrom pools of random-sequence oligonucleotides, with high bindingaffinities and specificities for a wide range of biomedically relevanttargets, suggesting a wide range of therapeutic utilities for aptamers(Keefe, Anthony D., Supriya Pai, and Andrew Ellington. “Aptamers astherapeutics.” Nature Reviews Drug Discovery 9.7 (2010): 537-550). Thesecharacteristics also suggest a wide range of uses for aptamers as drugdelivery vehicles (Levy-Nissenbaum, Etgar, et al. “Nanotechnology andaptamers: applications in drug delivery.” Trends in biotechnology 26.8(2008): 442-449; and, Hicke B J, Stephens A W. “Escort aptamers: adelivery service for diagnosis and therapy.” J Clin Invest 2000,106:923-928.). Aptamers may also be constructed that function asmolecular switches, responding to a que by changing properties, such asRNA aptamers that bind fluorophores to mimic the activity of greenfluorescent protein (Paige, Jeremy S., Karen Y. Wu, and Samie R.Jaffrey. “RNA mimics of green fluorescent protein.” Science 333.6042(2011): 642-646). It has also been suggested that aptamers may be usedas components of targeted siRNA therapeutic delivery systems, forexample targeting cell surface proteins (Zhou, Jiehua, and John J.Rossi. “Aptamer-targeted cell-specific RNA interference.” Silence 1.1(2010): 4).

By means of further guidance, and without limitation, in certainembodiments, the gRNA is a protected guide. Protected guides aredesigned to enhance the specificity of a Cas protein given individualguide RNAs through thermodynamic tuning of the binding specificity ofthe guide RNA to target nucleic acid. This is a general approach ofintroducing mismatches, elongation or truncation of the guide sequenceto increase/decrease the number of complimentary bases vs. mismatchedbases shared between a target and its potential off-target loci, inorder to give thermodynamic advantage to targeted genomic loci overgenomic off-targets. In certain embodiments, the guide sequence ismodified by secondary structure to increase the specificity of theCRISPR-Cas system and whereby the secondary structure can protectagainst exonuclease activity and allow for 3′ additions to the guidesequence. In certain embodiments, a “protector RNA” is hybridized to aguide sequence, wherein the “protector RNA” is an RNA strandcomplementary to the 5′ end of the guide RNA (gRNA), to thereby generatea partially double-stranded gRNA. In an embodiment of the invention,protecting the mismatched bases with a perfectly complementary protectorsequence decreases the likelihood of target binding to the mismatchedbasepairs at the 3′ end. In certain embodiments, additional sequencescomprising an extended length may also be present. [0004] Guide RNA(gRNA) extensions matching the genomic target provide gRNA protectionand enhance specificity. Extension of the gRNA with matching sequencedistal to the end of the spacer seed for individual genomic targets isenvisaged to provide enhanced specificity. Matching gRNA extensions thatenhance specificity have been observed in cells without truncation.Prediction of gRNA structure accompanying these stable length extensionshas shown that stable forms arise from protective states, where theextension forms a closed loop with the gRNA seed due to complimentarysequences in the spacer extension and the spacer seed. These resultsdemonstrate that the protected guide concept also includes sequencesmatching the genomic target sequence distal of the 20mer spacer-bindingregion. Thermodynamic prediction can be used to predict completelymatching or partially matching guide extensions that result in protectedgRNA states. This extends the concept of protected gRNAs to interactionbetween X and Z, where X will generally be of length 17-20 nt and Z isof length 1-30 nt. Thermodynamic prediction can be used to determine theoptimal extension state for Z, potentially introducing small numbers ofmismatches in Z to promote the formation of protected conformationsbetween X and Z. Throughout the present application, the terms “X” andseed length (SL) are used interchangeably with the term exposed length(EpL) which denotes the number of nucleotides available for target DNAto bind; the terms “Y” and protector length (PL) are usedinterchangeably to represent the length of the protector; and the terms“Z”, “E”, “E′” and EL are used interchangeably to correspond to the termextended length (ExL) which represents the number of nucleotides bywhich the target sequence is extended. An extension sequence whichcorresponds to the extended length (ExL) may optionally be attacheddirectly to the guide sequence at the 3′ end of the protected guidesequence. The extension sequence may be 2 to 12 nucleotides in length.Preferably ExL may be denoted as 0, 2, 4, 6, 8, 10 or 12 nucleotides inlength. In a preferred embodiment the ExL is denoted as 0 or 4nucleotides in length. In a more preferred embodiment the ExL is 4nucleotides in length. The extension sequence may or may not becomplementary to the target sequence. An extension sequence may furtheroptionally be attached directly to the guide sequence at the 5′ end ofthe protected guide sequence as well as to the 3′ end of a protectingsequence. As a result, the extension sequence serves as a linkingsequence between the protected sequence and the protecting sequence.Without wishing to be bound by theory, such a link may position theprotecting sequence near the protected sequence for improved binding ofthe protecting sequence to the protected sequence. Addition of gRNAmismatches to the distal end of the gRNA can demonstrate enhancedspecificity. The introduction of unprotected distal mismatches in Y orextension of the gRNA with distal mismatches (Z) can demonstrateenhanced specificity. This concept as mentioned is tied to X, Y, and Zcomponents used in protected gRNAs. The unprotected mismatch concept maybe further generalized to the concepts of X, Y, and Z described forprotected guide RNAs.

In certain embodiments, any of the nucleases, including the modifiednucleases as described herein, may be used in the methods, compositions,and kits according to the invention. In particular embodiments, nucleaseactivity of an unmodified nuclease may be compared with nucleaseactivity of any of the modified nucleases as described herein, e.g. tocompare for instance off-target or on-target effects. Alternatively,nuclease activity (or a modified activity as described herein) ofdifferent modified nucleases may be compared, e.g. to compare forinstance off-target or on-target effects.

Also provided herein are compositions for use in carrying out themethods of the invention. More particularly, non-naturally occurring orengineered compositions are provided which comprise one or more of theelements required to ensure genomic perturbation. In particularembodiments, the compositions comprise one or more of the (modified) DNAbinding protein, and/or a guide RNA. In particular embodiments, thecomposition comprises a vector. In further particular embodiments, thevector comprises a polynucleotide encoding a gRNA. In particularembodiments, the vector comprises two or more guide RNAs. Said two ormore guide RNAs may target a different target (so as to ensure multiplextargeting) or the same target, in which case the different guide RNAswill target different sequences within the same target sequence. Whereprovided in a vector the different guide RNAs may be under commoncontrol of the same promotor, or may be each be under control of thesame or different promoters.

EXAMPLES

The invention is further described in the following examples, which donot limit the scope of the invention described in the claims.

Materials and Methods

The CD5L monomer, CD5L dimer and CD5L:p40 heterodimer generations wereout-sourced to Biolegend under CDA. Briefly, to generate the CD5L:p40heterodimer, Cd51 and Il 12b (p40) were cloned into mammalian expressionvector through a linker: P40-linker 2-3 (SGGG)-CD5L with His tag.Similarly, CD5L monomer and dimer were generated by cloning CD5L withHis tag at C-terminus into a mammalian expression vector. The plasmidsare expressed in mammalian cell line and secreted CD5L:p40, CD5L(monomer and dimer) were purified and confirmed by gel electrophoresisand HPLC.

CD5L Sequence Cloned:

-   -   1 (maplfnlmla ilsifvgscf s)*esptkvqlv ggahrcegry evehngqwgt        vcddgwdrrd    -   61 vavvcrelnc gaviqtprga syqppaseqr vliqgvdcng tedtlaqcel        nydvfdcshe    -   121 edagaqcenp dsdllfiped vrlvdgpghc qgrvevlhqs qwstvckagw        nlqvskvvcr    -   181 qlgcgrallt ygscnkstqg kgpiwmgkms csgqeanlrs cllsrlennc        thgedtwmec    -   241 edpfelklvg gdtpcsgrle vlhkgswgsv cddnwgeked qvvckqlgcg        kslhpspktr    -   301 kiygpgagri wlddvncsgk eqslefcrhr lwgyhdcthk edvevictdf dv

*the signaling peptide was not included to better guide proteinsecretion in the expression system

p40/il 12b Sequence Cloned

-   -   1 mcpqkltisw faivllvspl mamwelekdv yvvevdwtpd apgetvnitc        dtpeedditw    -   61 tsdqrhgvig sgktltitvk efldagqytc hkggetlshs hlllhkkeng        iwsteilknf    -   121 knktflkcea pnysgrftcs wlvqrnmdlk fniksssssp dsravtcgma        slsaekvtld    -   181 qrdyekysys cqedvtcpta eetlpielal earqqnkyen ystsffirdi        ikpdppknlq    -   241 mkplknsqve vsweypdsws tphsyfslkf fvriqrkkek mketeegcnq        kgaflvekts    -   301 tevqckggnv cvqaqdryyn sscskwacvp crvrs

Recombinant protein CD5L monomer and homodimer was purified from thesupernanant of 293E cells transfected with a CD5L expression vector.Recombinant mCD5L:p40 was recovered from the supernatant of 293E cellstransfected with the CD5L:p40 expression vector. After harvestingtransfected 293E cells by centrifugation, the protein was affinitypurified from the supernatant using Ni Sepharose 6 Fast Flow resin (GEHealthcare). After binding the protein to resin, the resin was washedwith 20 mM Tris, 0.3M NaCl, pH 8.0 and the protein eluted using 20 mMTris, 0.3M NaCl, 0.4M Imidazole, pH 8.0. The protein was furtherpolished by a Superdex S200 sizing exclusion column (GE Healthcare) inbuffer 10 mM NaHPO4, 0.15M NaCl, pH 7.2. The S200 profile of themCD5L:p40 showed a single peak. The S200 profile of the mCD5Ltransfection showed two overlapping peaks, corresponding to thehomo-dimer fraction first and then monomer fraction

Example 1. Soluble CD5L and CD5L/p40 can Regulate T Cell Function andhave Overlapping as Well as Distinct Roles

CD5L can be secreted by macrophages (Miyazaki et al., 1999) and givenits T-cell intrinsic role, we tested the hypothesis that soluble CD5Lcan regulate T cell function directly in vitro. Although Abdi et al.reported that CD5L can form a heterodimer with p40, no specific functionwas attributed to this potential cytokine (Abdi et al., 2014). Wehypothesized that both soluble CD5L and CD5L:p40 heterodimer canregulate T cell function directly.

To this end, we used recombinant CD5L monomer either alone or withrecombinant p40 monomer and analyzed the transcriptome of activated CD4T cells, either WT or CD5L^(−/−), co-incubated with these solublefactors. First, we analyzed the effect of soluble CD5L alone. Wereasoned that if soluble CD5L (sCD5L) functions similarly to that ofT-cell intrinsic CD5L, the addition of sCD5L can reverse the effects ofCD5L deficiency on T cells. Indeed, we showed that sCD5L reversed theexpression profile of majority of genes differentially regulated by anyof the conditions tested (FIG. 1A). To exclude inference from T cellendogenous CD5L expression, we focused on the impact of sCD5L onCd5l^(−/−) cells. Of interest, sCD5L also regulated expression profileof genes that were not changed comparing WT and Cd5l^(−/−) cells oropposed the T-cell intrinsic function of CD5L (FIG. 1A), suggestingpotential novel role of the soluble CD5L.

Next, we performed pathway analysis of genes regulated by soluble CD5Land found sCD5L regulated gene profile contains both a regulatory and aninflammatory component. First, we observed that in sCD5L treated T cellsthere was a significant enrichment of signature genes of regulatory Tcells from four different datasets using MSigDB (Table 1). Interestinglythe key transcription factor of Treg, Foxp3, was downregulated by sCD5L(Table 1). This is consistent with sCD5L also promoting factors (such as114, 119) that have been implicated in destabilizing Foxp3 expressionantagonizing retinoic acid (Table 1 and (Hill et al., 2008)). These datasuggest that soluble CD5L may promote a regulatory program butindependent of Foxp3 expression and maybe an inducer of Th9 response. Inaddition to the regulatory component, we found that sCD5L regulatedgenes are significantly enriched for genes induced by IL-6/IL-1B butdownregulated by IL-6/IL-1B/IL-23, suggesting soluble CD5L mayantagonize IL-23 function (Table 1).

TABLE 1 Pathway analysis of soluble CD5L-dependent regulation of Tcells. Enriched pathways genes A. Reversal/Novel (soluble) UP Treg(PDL2, LIF, SOCS2, IKZF4, ICOS, (4 independent datasets) PROCR, NFIL3,CD200, TGM2, PRNP, (FDR q-value 1.63e−8) CD70, XBP1, ATF4, LAD1, KLF9,CD83, Runx2, IRF8, IFNg etc) RA treated memory CD4 IER3, IL4, RAB33A,FZD7, NFIL3, (FDR q-value 9.58e−10) SLAMF7, TNFSF9, FAIM3, IL9, Foxp3IL-6/IL-1B IL-22, GJA1, EGR2, IL1RN, CD200, ITGA3 IL-4 IL-4 B.Reversal/Novel (soluble) DOWN -IL-6/IL-1B/IL-23 GMFG, MGLL, FRMD4B, MINA

Soluble CD5L induces both a regulatory and proinflammatory programincluding 119 response. Differentially regulated genes were investigatedusing Msigdb and selected significant enrichment are listed in A and Bshowing those upregulated and downregulated by soluble CD5Lrespectively. Red and Green indicates directionality: Red pathway meanssoluble CD5L treatment goes with, green pathway means goes against suchpathways (In the above tables, the “Treg,” “IL-6/IL-1B,” and “IL-4” rowsare red pathways, and the “RA treated treated memory CD4” and“IL-6/IL-1B/IL-23” rows are green pathways).

Finally, we compared the effect of sCD5L to that of sCD5L:p40 and foundthese two cytokines to regulate the expression profile of both similarand distinct set of genes (FIG. 2). Thus, these data collectivelysuggest sCD5L and sCD5L:p40 are novel cytokines that can regulate T cellfunction.

Example 2. T Cell Regulation by sCD5L and CD5L:p40 Depends on IL-23RSignaling

As sCD5L and CD5L:p40 can regulate gene expression in T cells, weinvestigated what receptor(s) might be responsible for their function.CD5L was reported to interact with CD36, a scavenger receptor, and thuscan be internalized into adipocytes (Kurokawa et al., 2010). Weinvestigated whether CD36 is required for signaling of sCD5L in T cells.We showed that His-tagged sCD5L can stain WT and CD36^(−/−) T cellsequally well even at lower concentrations (FIG. 3A and data not shown).While this data is consistent with lower expression of CD36 on T cellscompared to macrophage (ImmGen database), it also raises the questionwhether the sCD5L can bind to a different receptor on T cells.

CD5L can form a heterodimer with p40 and p40 can bind to either p19 orp35. We hypothesized that if sCD5L binds to a surface receptor it may beco-regulated/dependent on receptors for the other two cytokines: that isIL-12RB1, IL-12RB2 or IL-23R. We tested whether sCD5L can stain Il12rb1^(−/−), Il 12rb2^(−/−) or Il 23r^(−/−) T cells as compared to WT(FIG. 3A and data not shown). Interestingly, the binding of sCD5L isabolished on Il 23r^(−/−) T cells and partially reduced on Il12rb1^(−/−), Il 12rb2^(−/−) T cells. These findings suggest that CD5Lmay interact with a receptor that depends on IL-23R signaling.

Next, we asked the question whether the function of sCD5L is alsoaffected by the absence of IL-23R on T cells. To this end, we crossedCd5l^(−/−) mice with Il23r^(−/−) mice and found that in the absence ofIL-23R, the expression of 89% of genes (84 out of 94 based on nanostringset) regulated by sCD5L were no longer affected (FIG. 3B). The effect ofCD5L:p40 heterodimer could also be partially dependent on IL-23Rexpression (FIG. 3C). Thus sCD5L and CD5L:p40 may interact withdifferent receptors on T cells.

Example 3. CD5L Regulates not Only T Cells but Also RestrainsProinflammatory Function of Innate Lymphoid Cells (ILC) and is Expressedby ILC in Naïve Mouse

The discovery that soluble CD5L can regulate T cell function directlyand that its impact may dependent on IL-23R expression prompted us tostudy whether CD5L can regulate other cells that may also expressIL-23R. To this end, we investigated the impact of CD5L on two suchpopulations that express IL-23R: innate lymphoid cells (ILC) anddendritic cells (DC).

First, we analyzed the percent and function of ILC in naïve 6-month oldWT versus Cd5l^(−/−) mice. We observed that IL-23R expression on ILCfrom lamina propria is significantly increased in the absence of CD5L(FIG. 4A). This is accompanied with higher proportion of ILCs producingIL-17 and Tbet, but lower percent of IL-22 producers (FIG. 4BC). Wefurther demonstrated that the reduced IL-22 expression and increasedTbet expression by ILC can be reverted by soluble CD5L ex vivo (FIG.4C). These data suggest that CD5L can regulate ILC function at steadystate. Of interest, we observed that ILC isolated from both mLN andlamina propria from naïve mice can express CD5L (FIG. 4D).

Next, we asked whether CD5L influence ILC during inflammation. As CD5Lregulates IL-17 and IL-17 production is associated with ILC3, we crossedCd5r′^(−/−) mice with fate mapping reporter miceIl17a^(Cre)Rosa26^(Td-tomato) to better track ILC3 that has evertranscribed sufficient IL-17 to turn on the Cre. Using the DSS-inducedacute colitis model, we showed that there is similar percent of Rosa26⁺ILC comparing 8-wk old WT.Il17a^(Cre)Rosa26^(Td-tomato) and Cd5l^(−/−)Il17a^(Cre)Rosa26^(Td-tomato) mice at day 11 since DSS treatment (FIG.4F), suggesting CD5L does not influence the differentiation of ILCsinitially. Consistently, the percent of ILC that expresses Rorgt is notsignificantly altered (FIG. 4E). In contrast to the Rosa26 expression,ILC from WT.Il17a^(Cre)Rosa26^(Td-tomato) make little IL-17 and turnedon IL-10 expression in striking contrast to those fromcd5l^(−/−)Il17a^(Cre)Rosa26^(Td-tomato) mice which continue to producemuch higher expression of IL-17 and are IL-10 negative (FIG. 4G). ThusCD5L can restrain proinflammatory function of ILC during acuteinflammation.

Example 4. CD5L:p40 Promotes Regulatory Programs in CD11c+ Cells in anIL-23R but not CD36 Dependent Manner

It has been reported that CD5L can induce autophagy in the humanmacrophage cell line, THP, limiting TNFa and IL-1B expression andpromoting IL-10 expression (Sanjurjo et al., 2015). The authors proposeCD36 is the major recipient of CD5L in these cells. As we discoveredthat sCD5L (and CD5L:p40 heterodimer) could regulate T cells through anIL-23R-dependent alternative receptor, we tested the hypothesis thatCD5L and CD5L:p40 may regulate myeloid cells in an IL-23R dependentpathway.

To test this hypothesis, we isolated WT, CD36^(−/−) and IL-23R^(−/−)CD11c⁺ cells from spleen of naïve mice and stimulated the cells with LPSin the presence of sCD5L, p40 or CD5L:p40. We showed that sCD4L, p40 andCD5L:p40 can all induce IL-10 expression from CD11c⁺ cells, however theeffect of CD5L:p40 is dependent on IL-23R whereas the effect of sCD5L isdependent on CD36 (FIG. 5).

Example 5. CD5L Plays a Protective Role in Acute Colitis and Cancer

To test the function of CD5L and CD5L:p40 in vivo, we tested severaldisease models. CD5L^(−/−) mice were treated with 2% DSS in drinkingwater for 6 days followed by normal water. Weight loss was reported as apercentage of initial weight in FIG. 6A. Colitis score and colon lengthwere determined on day 14, and are shown in FIGS. 6B and C,respectively. Colon histology on day 14 is shown in FIG. 6D. This datademonstrates that CD5L influenced tumor progression in a B16 melanomamodel.

Example 6. CD5L Ameliorates Autoimmune Diseases (Including MS), AcuteColitis, and Cancer

To show that CD5L:p40 can ameliorate disease, we therapeutically treatmouse models of multiple sclerosis (EAE), colitis (e.g., DSS-inducedinjury model which is a mouse model for ulcerative colitis and T-celldependent colitis model) or cancer (e.g., mice with inflammation-inducedcancers, or human cancer xenografted onto mice) with recombinantCD5L:p40, or antibodies or antigen-binding fragments thereof or thatbind to the heterodimers.

Example 7. Recombinant CD5L Binds to T Cells and Suppresses EAE andDSS-Induced Colitis

Experiments were conducted to assess whether soluble CD5L could regulateeffector T cells. In particular, soluble CD5L was directly evaluatedusing recombinant CD5L with a His-tag. Th0, Th1 (IL-12), and TH17p(IL-1b, IL-6, IL-23) cells were differentiated from naïve CD4 T cells invitro for 4 days, and cells were harvested for staining with recombinantCD5L followed by anti-His APC antibodies and flow cytometry analysis.Flow cytometry data showed that CD5L can bind to both Th1 and pathogenicTh17 cells (Th17p) and to a lesser extent Th0 cells (FIG. 7A). Thebinding of CD5L on T cells was shown to not require CD36, but to bedependent on IL-23R (e.g., loss of IL-23R abrogated CD5L binding to Tcells).

In vivo therapeutic experiments were conducted by immunizing wildtypemice with MOG/CFA following by PT injection to induce EAE. Mice at peakof disease (score=3 in FIG. 7B) were injected with either PBS (solidcircles) or recombinant CD5L (empty circles) intraperitoneally daily for5 consecutive days and mice were measured for disease progression. Asshown in FIG. 7B, soluble CD5L was shown to have a therapeutic effect onEAE.

In a separate experiment, wildtype mice were induced with colitis via2.5% DS in drinking water for 6 consecutive days, followed by normalwater for 8 days. Mice were given either a control (PBS) or recombinantCD5L (CD5Lm) intraperitoneally on day 4, 6, and 8. Colon length andcolitis score were recorded on day 14. As shown in FIG. 7C, recombinantCD5L was sufficient in alleviating colitis disease severity.

Example 8. Endogeneous CD5L Forms a Heterodimer (CD5L:p40) and isInducible During an Acute Inflammation

CD5L can bind to p40, the subunit shared by the cytokines IL-12 andIL-23, and form a heterodimer in vitro. This raises the intriguingpossibility that CD5L can generate different soluble mediators withpotentially distinct functions. To determine whether CD5L:p40heterodimer can be detected in vivo in biological settings, recombinantCD5L:p40 (FIG. 8A) was generated and used to optimize an ELISA thatallowed the detection of endogenous CD5L:p40 heterodimer.

Serum was collected kinetically from wildtype and Cd5l^(−/−) mice withDSS-induced colitis (2% DSS in drinking water for 6 days followed by 7days of normal water) and the level of CD5L:p40 was measured using anELISA assay. In the ELISA assay anti-IL-12 p40 was used to capture theheterodimer and enzyme linked anti-CD5L was used to detect theheterodimer. Data from this assay showed that natural CD5L:p40heterodimer was induced during the course of DSS-induced colitis inserum (FIG. 8B).

Example 9. IL-27 and TLR9 Induce CD5L Dimerization

Preliminary screens were conducted to determine what signals couldinduce CD5L homodimer and CD5L:p40 heterodimer. In particular, bonemarrow derived dendritic cells were stimulated with TLR ligands for 24hours and the supernatant was analyzed for CD5L:p40 secretion by ELISA.The screens showed that TLR9 can induce the secretion of CD5L:p40 (FIG.9A). To determine the signals that could induce CD5L on T cells, CD5Lexpression in Th0, Th1, Th2, Th17 and Tr1 cells was analyzed, and thedata showed that the immunosuppressive cytokine IL-27 can indeed induceCD5L (FIG. 9B and data not shown).

Example 10. CD5L Homo/Heterodimer Inhibits IL-17 Production and thePathogenic Th17 Cell Signature

To determine the function of CD5L homo/heterodimers on Th17 cellsdirectly, pathogenic Th17 cells (IL-1b+IL-6+IL-23) were treated witheither PBS (control), CD5L homodimers or CD5L:p40 heterodimers. IL-17expression of T cells was measuring by FACS (FIG. 10A), and IL-17production in serum was measured by ELISA (FIG. 10B). These experimentsshowed that both forms of CD5L inhibited IL-17 expression (FIGS. 10A-B).

To test whether recombinant CD5L can regulate the transcriptome of Th17cells and particularly the pathogenic signature, the RNA expression ofcontrol and treated cells was studied with a custom-code set of 337genes, and analyzed against signature genes of pathogenic Th17 cells(e.g., il23r, il22, il1r1, csf2) with GSEA, using the nanostringplatform. The signature of pathogenic Th17 cells was significantlyreduced by both CD5L:CD5L and CD5L:p40 as compared to a control (FIG. 10C (FDR q=0.031, NOM p=0.000, NES=−1.66) and 10D (FDR q=0.031, NOMp=0.000, NES=−1.47), respectively).

Example 11. CD5L Suppresses IL-17 and IFNg Expression from PathogenicTh17 Cells and Th1 Cells, Respectively

Pathogenic Th17 cells and Th1 cells were differentiated from naïve CD4cells (CD44^(low)CD62L⁺CD25-CD4⁺) from wildtype mice with IL-1b, IL-6,and IL-23 (Th17) or IL-12 (Th1) in the presence of a control, CD5Lhomodimer, or CD5L:p40 heterodimer for 48 hrs (Th17) or 72 hours (Th1).IL-27 expression in Th17 cells was measured by ELISA in supernatant(FIG. 11A, left side) and by qPCR from RNA purified from cells (FIG.11A, right side). IFNg expression in Th1 cells was measured byintracellular staining followed by flow cytometry analysis (FIG. 11B).The results showed that CD5L suppresses IL-17 and IFNg production inpathogenic T cells.

To assess pathogenic T cell signatures, RNA was extracted from both Th17and Th1 cells after 48 hours of differentiation. Extracted RNA wasanalyzed with a custom codeset of 337 genes using the nanostringplatform (four replicates for each conditions were measured). TheSpearman coefficient was used for clustering. A heat map ofdifferentially expressed genes as compared to control (defined byp<0.05) is shown in FIG. 12A for Th17 cells and FIG. 12B for Th1 cells(left panels). GSEA analysis against the pathogenic signatures are shownin the right panels of FIGS. 12A and B.

Example 12. Endogenous CD5L Promotes EAE Resolution and is Expressed byBoth Non-Pathogenic Th17 Cells and CD11b+ Cells During EAE Development

To determine which cells express CD5L during EAE, cd5l^(−/−) mice wereimmunized with MOG/CFA to induce EAE and followed for clinical scores.Th17 cells (IL-17.GFP+CD4+) and CD11b+ myeloid cells were sorted fromboth spleen and CNS of mice at peak disease (score=3). Mice with globalCD5L deficiency showed more severe and sustained EAE compared tocontrols (FIG. 13A), indicated that CD5L contributes to EAE resolution.

To assess CD5L expression in EAE, IL-17 GFP reported mice were immunizedwith MOG/CFA to induce EAE. Mice were sacrificed at peak of disease(score=3). Th17 cells were sorted based on CD4+GFP+ and macrophage weresorted based on CD11b+ from both the spleen and CNS of the mice. RNA waspurified from sorted cells and qPCR was used to measured CD5Lexpression. The experiments showed that CD5L was preferentiallyexpressed by Th17 cells in the spleen and by macrophage cells in the CNS(FIG. 13B).

Example 13. Generation of CD5L Conditional Knockout Mouse; Role in TumorImmunity

To study the cellular source of CD5L during EAE development, CD5Lflox/flox mice (CD5Lfl/fl) were generated by crossing FLPo mice and micethat were heterozygous with the construct shown in FIG. 14A (purchasedfrom EUCOMM/KOMP). The CD5L flox/flox mice were bred to homozygosity andcrossed with CD4-Cre, IL-17-Cre and LysM-Cre for conditional deletion ofthe Cre-loxP system. Representative genotyping results for CD5Lflox/flox mice are shown in FIG. 14B. CD5L^(fl/fl) mice weresuccessfully crossed with LysMCre, CD4Cre and IL-17Cre mice tospecifically delete CD5L in myeloid lineage cells, T cells andIL-17-producing cells respectively.

CD5L^(flox/flox)Lymz^(Cre+) (CD5L CKO) and CD5L^(flox/flox) mice wereinjected with 1×10⁶ MC38 colon carcinoma subcutaneously on the rightflank. Tumor size was measured up to 19 days post-injection, and isplotted in FIG. 15A. Pictures of mice sacrificed on day 19 post tumorcell injection are shown in FIG. 15B.

Example 14. CD5L and IL-23 Alter Lipidome of Th17 Cells in Correlationwith T Cell Function and EAE

Th17 cells were differentiated from naïve cells under pathogenic andnon-pathogenic conditions and harvested for LC/MS at 96 hours. Thelipidome of wildtype and Cd5l^(−/−) Th17 cells was analyzed. A strikingcorrelation of the lipidome of Th17 cells to their function and abilityto induce EAE was found (FIG. 16). In fact, Th17 cell function could bechanged based on alterations of the Th17 cell lipidome.

Example 15. Gene Expression Profile of Metabolic Pathways Correlateswith Th17 Cell Pathogenicity

To determine whether metabolic genes are differentially expressed at thetranscriptome level in Th17 cells with different functional state, themetabolic transcriptome in single cell RNAseq data was analyzed. Theanalysis showed metabolic transcriptome expression covariance with Th17cell pathogenicity (FIG. 17).

Example 16. CD5L Plays a Critical Role in Tumor Immunity, Regulating TCell Exhaustion

Littermate controls of CD5L^(+/−) and CD5L^(−/−) mice were grafted with1×10⁶ MC38 or MC38-OVA colon carcinoma subcutaneously on the rightflank, and then tumor progression was followed. Tumor size progressionfor MC38 and MC38-OVA experiments are shown FIGS. 18A and B,respectively. Tumor infiltrating lymphocytes were isolated from MC38 onday 30 and analyzed, and the results are shown in FIG. 19C. Tumorinfiltrating lymphocytes were isolated from MC38-OVA on day 14 andinculcated with OVA peptide or no peptide (control) for 20 hours.Brefaldin A and monensin was added in the last 4 hours and cytokineswere measured instracellularly by flow cytometry (see FIG. 19D). Theseresults demonstrate that CD5L deficiency inhibits T cell dysfunction andpromotes tumor suppression.

Example 17: Link Between CD5L:p40 Heterodimer and Tumor Progression

Litter mate controls of wildtype, CD5L^(+/+) and CD5L^(−/−) mice wereinjected with 1×10⁶ MC38 colon carcinoma subcutaneously on the rightflank, and CD5L:CD5L and CD5L:p40 were measured in serum during tumorprogression. Serum was obtained and measured for (a) CD5L:p40heterodimer using sandwich ELISA captured by anti-IL-12p40 antibody anddetected with biotinylated anti-CD5L antibody and (b) CD5L:CD5Lhomodimer using sandwich ELISA captured and detected by anti-CD5Lantibodies. Results are shown in FIGS. 19A-B.

Example 18: CD5L Suppresses Pathogenic T Cell Signatures

Pathogenic Th17 cells and Th1 cells were differentiated from naïve CD4 Tcells (CD44^(low)CD62L⁺CD25-CD4⁺) from wildtype mice with IL-1b, IL-6and IL-23 (Th17) in the presence of control, CD5L homodimer, or CD5L:p40heterodimer for 48 hours. RNA were extracted and subjected to RNAsequsing NextSeq. A heat map prepared from this data (FIG. 20; fourreplicates from each condition is shown; spearman coefficient was usedfor clustering) shows that the presence of CD5L:CD5L results inexpression of different signature genes than does the presence ofCD5L:p40. The heat map shows differentially expressed genes in theCD5L:CD5L and CD5L:p40 experiments as compared to the control(differentially expressed genes are defined by p<0.5 as compared tocontrol). This data demonstrates that both CD5L:CD5L and CD5L:p40 cansuppress pathogenic T cell signatures, but that the suppression viaCD5L:CD5L and CD5L:p40 is associated with expression of distinct cellsignatures.

Example 19: In Vivo Effect of CD5L:p40

To assess in vivo efficacy of CD5L dimers, wildtype mice were treatedwith 2% DSS in drinking water for 5 days, followed by normal water for 6days. Mice were injected with PBS, recombinant CD5L:CD5L, or recombinantCD5L:p40 intraperitoneally on days 4, 6, and 8. Cells from mesentericlymph nodes (mLN), peyer's patches (pp), lamina propria of colon (LP),and intraepithelial lymphocytes (IEL) were isolated, stained, andanalyzed directly with flow cytometry on day 11. The frequency ofFoxp3+CD4 T cells in various cell types is shown in FIG. 21A. Thefrequency of ILC3 as defined by CD45+Lineage-Thy1.2+CD127+Rorγt is shownin FIG. 21B. This data demonstrates that CD5L:p40 increased Tregs invivo in DSS-induced colitis.

Example 20: Generation of Anti-CD5L:CD5L Homodimer and Anti-CD5L:p40Heterodimer Antibodies

CD5L−/− mice were immunized with either recombinant CD5L:CD5L (labeled“714” in FIG. 22A) or recombinant CD5L:p40 (“711”, “712”) for antibodygeneration. Serum samples were taken from each mouse before spleeninfusion and tested for their ability to bind to either CD5L:p40 orCD5L:CD5L in a sandwich ELISA assay (FIG. 20A). B cells from the spleenof immunized mice were fused to generate pools of clones that wereallowed to expand. Serum from the pools were tested in the same ELISAassay. Polyclonal antibody pools that have preferential specificity toeither CD5L:p40 or CD5L:CD5L were observed (FIG. 22B).

It is contemplated that human antibodies CD5L:CD5L and CD5L:p40 can beprepared based on the degree of homology between mouse and human CD5Land p40 (FIGS. 23A and C). Also shown are homology between mouse andhuman protein sequences in p19 and p35 (FIGS. 23B and D), which can forma dimer with p40.

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OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method of suppressing an immune response in asubject, the method comprising administering to the subject atherapeutically effective amount of: a recombinant soluble CD5L:p40heterodimer and/or nucleic acids encoding CD5L and p40; (ii) arecombinant soluble CD5L:CD5L homodimer and/or a nucleic acid encoding aCD5L homodimer; and/or (iii) a recombinant soluble CD5L and/or a nucleicacid encoding CD5L.
 2. The method of claim 1, wherein the subject has anautoimmune disease.
 3. The method of claim 2, wherein the autoimmunedisease is Multiple Sclerosis (MS), Irritable Bowel Disease (IBD),Crohn's disease, spondyloarthritides, Systemic Lupus Erythematosus(SLE), Vitiligo, rheumatoid arthritis, psoriasis, Sjögren's syndrome, ordiabetes.
 4. The method of claim 1, wherein the subject has aninflammation-related cancer.
 5. The method of claim 4, wherein theinflammation-related cancer is colorectal cancer, carcinogen-inducedskin papilloma, fibrosarcoma, or mammary carcinomas.
 6. The method ofclaim 1, comprising administering the CD5L:p40 heterodimer.
 7. Themethod of claim 1, comprising administering the CD5L:CD5L homodimer. 8.A method of enhancing an immune response in a subject, the methodcomprising administering to the subject a therapeutically effectiveamount of an agent that: (a) inhibits a CD5L:p40 heterodimer, aCD5L:CD5L homodimer, and/or CD5L from binding to an IL-23 receptor;and/or (b) inhibits formation of the CD5L:p40 heterodimer and/or theCD5L:CD5L homodimer.
 9. The method of claim 8, wherein the agentcomprises an antibody, or an antigen binding fragment thereof, thatbinds to one or more of the CD5L:p40 heterodimer, the CD5L homodimer,and the CD5L.
 10. The method of claim 8, wherein the agent comprisesinhibitory nucleic acids that target the CD5L and/or the p40.
 11. Themethod of claim 8, wherein the subject has cancer that is notinflammation related.
 12. The method of claim 11, further comprisingadministering an anti-cancer immunotherapy to the subject.
 13. Themethod of claim 12, wherein the anti-cancer immunotherapy is selectedfrom the group consisting of checkpoint inhibitors, PD-1/PDL-1,anti-cancer vaccines, adoptive T cell therapy, and combinations of twoor more thereof.
 14. The method of claim 10, wherein the inhibitorynucleic acids are small interfering RNAs (e.g., shRNA), antisenseoligonucleotides, and/or CRISPR-Cas.
 15. The method of claim 8, whereinthe subject has an immune deficiency, e.g., a primary or secondaryimmune deficiency.
 16. The method of claim 8, wherein the subject has aninfection with a pathogen, e.g., viral, bacterial, or fungal pathogen.17. A method of modulating CD8⁺ T cell exhaustion in a subject in needthereof, the method comprising administering to the subject atherapeutically effective amount of an agent that: (a) inhibits aCD5L:p40 heterodimer, a CD5L:CD5L homodimer, and/or CD5L from binding toan IL-23 receptor; and/or (b) inhibits formation of the CD5L:p40heterodimer and/or the CD5L:CD5L homodimer.
 18. The method of claim 17,wherein said administering reduces CD8⁺ T cell exhaustion.
 19. Themethod of claim 17, wherein the subject has cancer.
 20. The method ofclaim 19, wherein the cancer is a non-inflammatory cancer.